Outline with details for Ab Stat Section expanded 11-8-13

2015-01-13

Outline with details for AbStat Section

aka Outline with details for AbStat Section expanded 11-8-13

See also
[Summary of different datasets as of 6-20-13]

-Introduction
{
--Fundamental Question
When sera antibodies react with an array of random peptides, each peptide will exhibit a different level of binding quantified as a peptide intensity.  The distribution of peptide intensities will depend on the number of different antibodies and their affinities and avidities for various peptide sequences.  The number of antibodies, the affinities of the antibodies, and the avidities of the antibodies will depend on the state of the organism: healthy or disease and young or old.  Can the information acquired from the peptide intensity distribution resulting from sera antibodies reacting with an array of random sequence peptides be used to distinguish healthy or disease states?  Can this information be compressed into a single quantified variable?

--Description of platform (reference Rebecca's papers)

-Entropy with previous biological data
--most of my notes for this section are found with in the "misc notes pre ...." text files on the day in which I did the work
--[Malaria in Africa Vector Species’ Niche Models and Relative Risk Maps]
--[Onset of Immune Senescence Defined by Unbiased Pyrosequencing of Human Immunoglobulin mRNA Repertoires]
--Correlation of antibody affinity (and avidity?) with disease and age
---Papers
----Effects of age on antibody affinity maturation.
-----http://www.ncbi.nlm.nih.gov/pubmed/12653658
----Antibody quality in old age.
-----http://www.ncbi.nlm.nih.gov/pubmed/16608408
----Effect of age on humoral immunity, selection of the B---cell repertoire and B---cell development.
-----http://www.ncbi.nlm.nih.gov/pubmed/9476670
---Increase of autoimmune disease with age

--Single number measures
---formatted entropy equations
----"C:\Users\kurtw_000\Documents\kurt\storage\CIM Research Folder\DR\2013\11-18-13\formatted entropy equations shannon and boltzmann 11-18-13.docx"
---characteristics of single number measures: entropy, kurtosis, skew, etc.
---Paper: Entropy Measures Quantify Global Splicing Disorders in Cancer (I found some other papers related to this paper as well)
----see also: [Biological Entropy Review 01-11-2014d1736]
---min and max of entropy, normalized entropy, entropy doesn't change with normalized values
---How is physics entropy, information entropy, and peptide intensity entropy related?

--Use for diagnosis and monitoring

}
-</Introduction>

-Materials and Methods
{
--Description of array production
---The 10K platform should be called CIM10k and the 330K platform should be called HT330k
--Description of array procedures
---The 330K methods came from here
"C:\Users\kurtw_000\Documents\kurt\storage\CIM Research Folder\DR\2013\11-19-13\Scalable High-Density Peptide Arrays for Comprehensive Health Monitoring Chip paper 7 (2) jbl 13AUG2013.docx"

The 10K methods came from here
"C:\Users\kurtw_000\Documents\kurt\storage\CIM Research Folder\DR\2013\11-1-13\Normals paper (2012)\Normals paper 2012 - formatted to journal specifications.dotx"

--Array procedures with samples

--Description of mathematical measures
---the formatted formulas for the mathematical measures are found from here: [list of summary numbers calculated by entropy program as of 10-9-13] (wikidpad)
--Description of Java program
---Optimization of Java program
--Description of Methods of analysis
---box and dotplots
---Student's T test
---SVM classification algorithm
---Classification tree
---Heirarchical clustering and heatmaps
---Software used: Custom Java program, Deducer, JMP, Excel
}
-</Materials and Methods>

-Results
{
--AbStat Changes with Artificial Antibody Experiments (Are there changes in the AbStat measurement with artificial antibody experiments?)
---Spiking antibody into sera (mouse and human)
{
antibody into normal mouse sera
{
-Entropy for increasing concentrations of a-GFOD1 antibody into normal mouse sera (aka Entropy for increasing antibody concentrations in normal mouse sera)
-Mean for increasing concentrations of normal mouse sera
--"C:\Users\kurtw_000\Documents\kurt\storage\CIM Research Folder\DR\2013\10-14-13\summary\table_of_summary_numbers with classification 10-14-13.xls"
}

antibody into normal human sera
{

-Entropy for increasing concentrations to 1 nM in normal human sera
-Entropy for increasing concentrations of a–gp120 antibody into normal human sera (aka Entropy for increasing concentrations to 100 nM in normal human sera)
-Mean for increasing concentrations to 1 nM in normal human sera
-Mean for increasing concentrations to 100 nM in normal human sera
-"C:\Users\kurtw_000\Documents\kurt\storage\CIM Research Folder\DR\2013\11-5-13\Antibody mix experiment from heidi and bart\table_of_summary_numbers 11-5-13.xlsx"

Each sample was ran in duplicate.. so I guess there should be two GPR's for each concentration. 
Also, the secondary we used was: pAB anti-Human IgG NB120-6758 Lot 2102. The Tertiary was: strepavidin-AF647 Lot 1081876 012512. These were incubated on the array at 5nM.

The antibody used was B12 which is to a protein on HIV (gp120)

(old)TODO
-I may want to go back and add Kd information and approximations in the discussion.(old)
}

}
---</Spiking antibody into sera>
---<Monoclonal affinity data> (aka Monoclonal affinities and AbStat Measures)
{
Both "b" and "t" samples were used

Figures
-Entropy of antibodies versus affinity for cognate sites (aka Entropy of antibodies with affinity records)
-Mean fluorescence of antibodies versus affinity for cognate sites (aka Mean of antibodies with affinity records)
-Heatmap of AbStat measures for antibodies versus affinity for cognate sites (aka Heatmap of AbStat measures for antibodies with affinity records) (this spreadsheet also contains the line graph)
--"C:\Users\kurtw_000\Documents\kurt\storage\CIM Research Folder\DR\2013\10-16-13\Rebecca Monoclonal Data\data\summary\antibody affinity cell plot formatted 4 04-08-2014d1703.png"
--"C:\Users\kurtw_000\Documents\kurt\storage\CIM Research Folder\DR\2013\10-16-13\Rebecca Monoclonal Data\data\summary\antibody affinity cell plot formatted 04-08-2014d1657.svg"
--"C:\Users\kurtw_000\Documents\kurt\storage\CIM Research Folder\DR\2013\10-16-13\Rebecca Monoclonal Data\data\summary\table_of_summary_numbers with classification 10-16-13.xls"
-Histogram and box plot for 80 nM Kd antibody
--data from this gpr: b-cMyc_111610_AMI110210-14_SLOT05_S01_H_newGAL.gpr
--minimum bin width that could be set was 140
--"C:\Users\kurtw_000\Documents\kurt\storage\CIM Research Folder\DR\2013\10-16-13\Rebecca Monoclonal Data\data\summary\histograms\histograms 2\cMyc 80nM Kd histogram 01-06-2014d1425.jrp"
--"C:\Users\kurtw_000\Documents\kurt\storage\CIM Research Folder\DR\2013\10-16-13\Rebecca Monoclonal Data\data\summary\histograms\histograms 2\cMyc 80nM Kd histogram 01-06-2014d1425.svg"
--"C:\Users\kurtw_000\Documents\kurt\storage\CIM Research Folder\DR\2013\10-16-13\Rebecca Monoclonal Data\data\summary\histograms\histograms 2\cMyc 80nM Kd histogram 01-06-2014d1425.png"

-Histogram and box plot for <0.1 nM Kd antibody
--data from this gpr: b-P53Ab1_111610_AMI110210-16_SLOT09_S01_H_newGAL.gpr
--minimum bin width that could be set was 140
--"C:\Users\kurtw_000\Documents\kurt\storage\CIM Research Folder\DR\2013\10-16-13\Rebecca Monoclonal Data\data\summary\histograms\histograms 2\p53 less than 0p1 nM ab 01-06-2014d1601.jrp"
--"C:\Users\kurtw_000\Documents\kurt\storage\CIM Research Folder\DR\2013\10-16-13\Rebecca Monoclonal Data\data\summary\histograms\histograms 2\p53 less than 0p1 nM ab 01-06-2014d1613.svg"
--"C:\Users\kurtw_000\Documents\kurt\storage\CIM Research Folder\DR\2013\10-16-13\Rebecca Monoclonal Data\data\summary\histograms\histograms 2\p53 less than 0p1 nM ab 01-06-2014d1621.png"

Questions
{
?What was the concentration of antibody used in Rebecca's monoclonal antibody experiment?  She applied the anti-h-cMyc antibody, the anti-h-proenkephalin-B antibody, and the anti-h-p53 antibody to the array.
-From Bart as of 12-11-2013d1520: Depends on which arrays these were.  She tended to use 5 to 100 nM with the most common range 5 to 10 nM.
-I emailed Rebecca about the issue 12-11-2013d1538
}

}
---</Monoclonal affinity data>
---<Mixing two monoclonal antibodies>
{
graphs and data found here
-C:\Users\kurtw_000\Documents\kurt\storage\CIM Research Folder\DR\2013\10-23-13\Monoclonal ab data\summary of all monoclonal ab 330k results

-Histogram of antibodies ((Histogram and boxplots for Ab1 in A), Ab2 in B), and Ab1 mixed with Ab2 in C)) renamed to (Histogram and boxplots for Ab1 and Ab2))
--ab1
---data from here: "C:\Users\kurtw_000\Documents\kurt\storage\CIM Research Folder\DR\2013\10-23-13\Monoclonal ab data\ab mix experiment\p53Ab1\HT4-25 S6 D2 GRN-P80 RED P50 062113 p53Ab1_0532 SM.gpr"
---"C:\Users\kurtw_000\Documents\kurt\storage\CIM Research Folder\DR\2013\10-23-13\Monoclonal ab data\ab mix experiment\histograms\ab1 Distribution 01-06-2014d1647.jrp"
---"C:\Users\kurtw_000\Documents\kurt\storage\CIM Research Folder\DR\2013\10-23-13\Monoclonal ab data\ab mix experiment\histograms\ab1 Distribution 01-07-2014d1055.svg"
---"C:\Users\kurtw_000\Documents\kurt\storage\CIM Research Folder\DR\2013\10-23-13\Monoclonal ab data\ab mix experiment\histograms\ab1 histogram 01-07-2014d1107.png"
--ab2
---data from here: "C:\Users\kurtw_000\Documents\kurt\storage\CIM Research Folder\DR\2013\10-23-13\Monoclonal ab data\ab mix experiment\p53Ab8\HT4-25 S6 E2 GRN-P80 RED P50 062113 p53Ab8_0532 SM.gpr"
---"C:\Users\kurtw_000\Documents\kurt\storage\CIM Research Folder\DR\2013\10-23-13\Monoclonal ab data\ab mix experiment\histograms\ab2 Distribution 01-06-2014d1647.jrp"
---"C:\Users\kurtw_000\Documents\kurt\storage\CIM Research Folder\DR\2013\10-23-13\Monoclonal ab data\ab mix experiment\histograms\ab2 Distribution 01-07-2014d1055.svg"
---"C:\Users\kurtw_000\Documents\kurt\storage\CIM Research Folder\DR\2013\10-23-13\Monoclonal ab data\ab mix experiment\histograms\ab2 Distribution 01-07-2014d1055.png"
--ab1 & ab2 mix
---data from here: "C:\Users\kurtw_000\Documents\kurt\storage\CIM Research Folder\DR\2013\10-23-13\Monoclonal ab data\ab mix experiment\mAbmix\HT4-25 S6 F1 GRN-P80 RED P50 062113 mAbmix_0532 A.gpr"
---"C:\Users\kurtw_000\Documents\kurt\storage\CIM Research Folder\DR\2013\10-23-13\Monoclonal ab data\ab mix experiment\histograms\mab mix 01-07-2014d1651.jrp"
---"C:\Users\kurtw_000\Documents\kurt\storage\CIM Research Folder\DR\2013\10-23-13\Monoclonal ab data\ab mix experiment\histograms\abmix Distribution 01-07-2014d1055.svg"
---"C:\Users\kurtw_000\Documents\kurt\storage\CIM Research Folder\DR\2013\10-23-13\Monoclonal ab data\ab mix experiment\histograms\abmix distribution 01-07-2014d2219.png"

questions
{
What was the concentration of each antibody used separately, and the concentration of each when used together?  What was the secondary antibody and dye used? (old; I found this information later)
}
}
---</Mixing two monoclonal antibodies>
--Mouse vaccines and infections (Are there changes in the AbStat measurement with artificial mouse vaccines and infections?)
{
---Bart's mouse infection data (three different experiments)
----mouse infection data
----survival records
----some mice with good vaccine and some mice with partial protection
----<246 day timecourse>
{
Heatmap of AbStat measures for 246 day mouse timecourse (Heatmap of AbStat measures for 246 day mouse timecourse with 2-3 technical replicates for each timepoint)
-"C:\Users\kurtw_000\Documents\kurt\storage\CIM Research Folder\DR\2013\11-7-13\Mouse Infection Long Timecourse\Mouse Infection Long Timecourse Cell Plot 4 04-08-2014d1734.png"
-"C:\Users\kurtw_000\Documents\kurt\storage\CIM Research Folder\DR\2013\11-7-13\Mouse Infection Long Timecourse\Mouse Infection Long Timecourse 2 04-08-2014d1728.svg"
TODO (old as of 04-08-2014d1737): fix the heatmap so that it does not have normalized entropy normalized data

Linegraph of entropy over time for 246 day mouse timecourse
"C:\Users\kurtw_000\Documents\kurt\storage\CIM Research Folder\DR\2013\11-7-13\Mouse Infection Long Timecourse\Mouse Infection Long experiment table of summary numbers 11-7-13.xlsx"

Statistical significance of measures comparing day 0 with day 256
"C:\Users\kurtw_000\Documents\kurt\storage\CIM Research Folder\DR\2013\11-7-13\Mouse Infection Long Timecourse\Mouse Infection Long experiment table of summary numbers 11-7-13.xlsx"

Weights of mice after infection in 246 day timecourse experiment
"C:\Users\kurtw_000\Documents\kurt\storage\CIM Research Folder\DR\2013\11-7-13\Mouse Infection Long Timecourse\mouse weights\EXP 642-102 Low Dose Vaccine Timecourse weights modified version.xls"

-{5}
<questions>
{
?How many mice were there in the 246 day timecourse (A: 10)?  What strain were they?  What age were they when they were infected?  What was the strain of influenza? Which arrays were these samples applied to?  When were the weights collected? (old; Bart answered these questions)
}
</questions>
-{5}

}
----<246 day timecoure>

-{4}<multiple mouse immunizations>
{
figures
-Entropy for multiple mouse immunization experiment
-Dynamic range for multiple mouse immunization experiment
-Figure 6 Bar graph of SVM weight for measures from multiple mouse immunization experiment
---"C:\Users\kurtw_000\Documents\kurt\storage\CIM Research Folder\DR\2013\11-5-13\Mouse Infection Experiment\Infected vs Mock on V3\table_of_summary_numbers Infected vs Mock on V3.xlsx"

Questions
?Which strain of influenza were the mice infected with?  What is a more proper term for "killed PR8"?  How was the mock group of mice treated (were they injected with PBS?  Was the sera taken on day 37 or 38?  What was the exact composition of the vaccines? (old; Bart answered these questions)
}
-{4}</multiple mouse immunizations>

-{4}<6 day timecourse>
{
figures
-Entropy for 6 day mouse timecourse
-Mean for 6 day mouse timecourse
"C:\Users\kurtw_000\Documents\kurt\storage\CIM Research Folder\DR\2013\11-5-13\Mouse Infection Experiment\Time Course on Version 1\mouse infection timecourse v1 11-8-13.xlsx"

questions:
How many mice were there?  What strain?  What were they infected with?  When did they die? How was the mock group treated? (old; Bart answered these questions)
}
-{4}</6 day timecourse>

}
--</Mouse vaccines and infections>
--<Human vaccination data> (Are there changes in the AbStat measurement with human vaccination data?)
{
---Human time course data

Data and graphs here (aka Daily one month entropy change and Change in entropy after vaccination)
--- "F:\kurt\storage\CIM Research Folder\DR\2013\10-19-13\normal_timecourse\summary\table_of_summary_numbers with classification 10-19-13.xls"
--- "F:\kurt\storage\CIM Research Folder\DR\2013\10-19-13\normal_timecourse\summary\table of summary numbers with classification for one month 10-26-13.xlsx"

Questions
{
Which type of array was each sample run on? (this array question may not be that relevant)  What was the name of the influenza vaccine they received?
}

TODO
{
-make color legend missing on one of the heatmaps (old)
-find out what HP disease is; I think it might be hepatitis C virus (old; hp was just unlabeled human plasma (I found out which disease or normal classification they were later)
-make names of samples consistent between datasets and figures. (old)
}
}
--</Human vaccination data>
--<Reduction in antibody repertoire complexity with lymphoma> (Are there changes in the AbStat measurement during the course of a lymphoma which reduces the complexity of the antibody repertoire?  During the course of a B cell lymphoma one particular antibody in the repertoire becomes dominant as one B cell proliferates uncontrollably and produces large amounts of the antibody) (LSA dog section)
{
data and figures found here
-"Box and dotplot of entropy for normal (N) and lymphosarcoma (LSA) dogs"
--"C:\Users\kurtw_000\Documents\kurt\storage\CIM Research Folder\DR\2013\10-19-13\bart_dog_lymphoma1\summary\classification vs entropy box and dotplot 11-12-13.png"
"C:\Users\kurtw_000\Documents\kurt\storage\CIM Research Folder\DR\2013\10-19-13\bart_dog_lymphoma1\summary\table_of_summary_numbers with classification 10-19-13d0856.xls"

---Bart's dog lymphoma data

questions
{
-How many dogs were used?  What type of dog?  Male or female?  What age? (old; Bart answered these questions)
-Why do I have two different dog lymphoma datasets? (they were just collected at different times)
}

}
--</Reduction in antibody repertoire complexity with lymphoma>

--<Mouse cancer progression data> (Are there changes in the AbStat measurement as mice develop cancer?)
{
location of data
"C:\Users\kurtw_000\Documents\kurt\storage\CIM Research Folder\DR\2013\11-12-13\FVBN Time Series\Entropy analysis for 2013 pilot study.xlsx"
---This spreadsheet contains this figure: Entropy timecourse for transgenic mouse

questions
What are the details of the cancer mice?  What strain are they?  What type of cancer do they develop, and when does this occur?  How many mice were in each group?  Is there a good paper I should reference that describes the mice? (old; I found this out from Tiger)
^questions answered
}
--<\Mouse cancer progression data>
--Human disease data (Can the AbStat measurements distinguish between humans with and without disease on different platforms?)
{
---330K wafer data
{
First chip disease dataset tables and figures
{
Box and dotplot of entropy for groups in first chip disease dataset
"C:\Users\kurtw_000\Documents\kurt\storage\CIM Research Folder\DR\2013\10-13-13\disease data from josh\results\summary\first chip disease dataset box and dot plot no hnp 111413d1108.png"

Heatmap of Measures for samples in first chip disease dataset
"C:\Users\kurtw_000\Documents\kurt\storage\CIM Research Folder\DR\2013\10-13-13\disease data from josh\results\summary\first chip disease dataset no hnp heatmap heirarchical cluster with key 111413d1142.png"

Statistical significance of measures comparing normal with disease in first chip disease dataset
"C:\Users\kurtw_000\Documents\kurt\storage\CIM Research Folder\DR\2013\10-13-13\disease data from josh\results\summary\first chip disease dataset clean 11-13-13.xlsx"

SVM weight of measures comparing normal with disease in first chip disease dataset
"C:\Users\kurtw_000\Documents\kurt\storage\CIM Research Folder\DR\2013\10-13-13\disease data from josh\results\summary\first chip disease dataset clean 11-13-13.xlsx"

J48graft tree for first chip disease dataset
"C:\Users\kurtw_000\Documents\kurt\storage\CIM Research Folder\DR\2013\10-13-13\disease data from josh\results\summary\machine learning\j48graft tree no hnp equal d and n 111413d1419.PNG"

Machine learning statistics for first chip disease dataset
"C:\Users\kurtw_000\Documents\kurt\storage\CIM Research Folder\DR\2013\10-13-13\disease data from josh\results\summary\first chip disease dataset clean 11-13-13.xlsx"

Machine learning statistics for first chip disease dataset with half samples as training rather than 10 fold cross-validation
"C:\Users\kurtw_000\Documents\kurt\storage\CIM Research Folder\DR\2013\10-13-13\disease data from josh\llnl specific peptide analysis\AbStat half training half test\machine learning statistics 01-28-2014d1602.xlsx"
}

wafer 46 tables and figures
{
box and dotplot (Box and dotplot of entropy for groups on wafer 46)
"C:\Users\kurtw_000\Documents\kurt\storage\CIM Research Folder\DR\2013\9-10-13\entropy\new summary 10-12-13\box and dotplot clean 11-12-13d1725.png"

heatmap
"C:\Users\kurtw_000\Documents\kurt\storage\CIM Research Folder\DR\2013\9-10-13\entropy\new summary 10-12-13\wafer 46 clean heatmap Hierarchical Cluster.png"

p-value bar chart
"C:\Users\kurtw_000\Documents\kurt\storage\CIM Research Folder\DR\2013\9-10-13\entropy\new summary 10-12-13\table_of_summary_numbers_clean 11-12-13.xlsx"

svm bar chart
-"C:\Users\kurtw_000\Documents\kurt\storage\CIM Research Folder\DR\2013\9-10-13\entropy\new summary 10-12-13\corrected_values_111313\table_of_summary_numbers_with_classification 111413d0928.xls"
--"C:\Users\kurtw_000\Documents\kurt\storage\CIM Research Folder\DR\2013\9-10-13\entropy\new summary 10-12-13\table_of_summary_numbers_clean 11-12-13.xlsx"
}
} 
---LLNL 10K dataset
10K LLNL tables and figures
{
boxplot
Box and dotplot of entropy for groups on CIM10K (aka Box and dotplot of entropy for groups on 10K)
-"C:\Users\kurtw_000\Documents\kurt\storage\CIM Research Folder\DR\2013\12-5-13\new analysis with knowledge of hp samples 12-05-2013d1022\10k llnl box and dotplot 12-05-2013d1123.png"
-older box and dotplot
"C:\Users\kurtw_000\Documents\kurt\storage\CIM Research Folder\DR\2013\10-17-13\id some on both arrays\10k llnl\summary\10k llnl box and dotplot clean 11-13-13d1301.png"

heatmap
(Heatmap of Measures for samples on CIM10K) (aka Heatmap of Measures for samples on 10K)
-"C:\Users\kurtw_000\Documents\kurt\storage\CIM Research Folder\DR\2013\12-5-13\new analysis with knowledge of hp samples 12-05-2013d1022\10k llnl heatmap with label 12-05-2013d1139.png"
-old
-"C:\Users\kurtw_000\Documents\kurt\storage\CIM Research Folder\DR\2013\10-17-13\id some on both arrays\10k llnl\summary\10k llnl heatmap Hierarchical Cluster 11-13-13d1349.png"

p-value bar graph
Statistical significance of measures comparing normal with disease for CIM10K (aka Statistical significance of measures comparing normal with disease for 10K)
-"C:\Users\kurtw_000\Documents\kurt\storage\CIM Research Folder\DR\2013\12-5-13\new analysis with knowledge of hp samples 12-05-2013d1022\table of summary numbers clean 12-05-2013d1027.xlsx"
-old one
"C:\Users\kurtw_000\Documents\kurt\storage\CIM Research Folder\DR\2013\10-17-13\id some on both arrays\10k llnl\summary\table_of_summary_numbers with classification clean 10-18-13.xlsx"

SVM bar graph
SVM weight of measures comparing normal with disease for CIM10K (aka SVM weight of measures comparing normal with disease for 10K)
"C:\Users\kurtw_000\Documents\kurt\storage\CIM Research Folder\DR\2013\12-5-13\new analysis with knowledge of hp samples 12-05-2013d1022\table of summary numbers clean 12-05-2013d1027.xlsx"
-old graph
"C:\Users\kurtw_000\Documents\kurt\storage\CIM Research Folder\DR\2013\10-17-13\id some on both arrays\10k llnl\summary\table_of_summary_numbers with classification clean 10-18-13.xlsx"

Tree
J48graft tree for CIM10K (aka J48graft tree for 10K)
"C:\Users\kurtw_000\Documents\kurt\storage\CIM Research Folder\DR\2013\12-5-13\new analysis with knowledge of hp samples 12-05-2013d1022\machine learning\j48graft tree 10k llnl 12-05-2013d1400.PNG"
-old
"C:\Users\kurtw_000\Documents\kurt\storage\CIM Research Folder\DR\2013\10-17-13\id some on both arrays\10k llnl\summary\machine learning\machine learning clean\j48graft tree 20n 20d.PNG"

Table of statistics
Machine learning statistics for CIM10K (aka Machine learning statistics for 10K)
"C:\Users\kurtw_000\Documents\kurt\storage\CIM Research Folder\DR\2013\12-5-13\new analysis with knowledge of hp samples 12-05-2013d1022\table of summary numbers clean 12-05-2013d1027.xlsx"
-old
"C:\Users\kurtw_000\Documents\kurt\storage\CIM Research Folder\DR\2013\10-17-13\id some on both arrays\10k llnl\summary\table_of_summary_numbers with classification clean 10-18-13.xlsx"
}

--<Alzheimer's data>  (Can the AbStat measurement distinguish between aged humans with alzheimers and aged human controls?)
{
graphs and data
{
Table of Machine learning statistics for Alzheimer's disease with specific peptide analysis
"C:\Users\kurtw_000\Documents\kurt\storage\lgdata_DR\2014\01-11-2014d1500\alz analysis\specific peptide anal half train half test\table of machine learning statistics.xlsx"

Box and dotplot of entropy for groups for Alzheimer's disease
"C:\Users\kurtw_000\Documents\kurt\storage\CIM Research Folder\DR\2013\10-17-13\alzheimers data\summary\graphs\entropy.tiff"

Heatmap of Measures for Alzheimer's disease
"C:\Users\kurtw_000\Documents\kurt\storage\CIM Research Folder\DR\2013\10-17-13\alzheimers data\summary\alzheimer's heatmap 111413d2217.png"

Statistical significance of measures comparing normal with Alzheimer's disease
"C:\Users\kurtw_000\Documents\kurt\storage\CIM Research Folder\DR\2013\10-17-13\alzheimers data\summary\table_of_summary_numbers with classification.xls"

Machine learning statistics for wafer 46
"C:\Users\kurtw_000\Documents\kurt\storage\CIM Research Folder\DR\2013\10-17-13\alzheimers data\summary\table_of_summary_numbers with classification.xls"
}
}
--</Alzheimer's data>
}
--</Human disease data>
--Changes with Age (Can the AbStat measurement be used to distinguish between young and aged organisms?)
---<Mouse young and old> 
{
aka Changes with age in mice
Mouse young and old graphs
{

Box and dotplot of entropy for young and aged mice (Young and aged mouse fluorescence intensity histograms)
"C:\Users\kurtw_000\Documents\kurt\storage\CIM Research Folder\DR\2013\9-26-13\old and young mice gpr files\summary\table_of_summary_numbers_clean_graph_100913d1421.png"

Heatmap of Measures for young and aged mice
"C:\Users\kurtw_000\Documents\kurt\storage\CIM Research Folder\DR\2013\9-26-13\old and young mice gpr files\summary\young and aged mice heatmap Hierarchical Cluster 11-15-13d0919.png"

Statistical significance of measures comparing young and aged mice
"C:\Users\kurtw_000\Documents\kurt\storage\CIM Research Folder\DR\2013\9-26-13\old and young mice gpr files\summary\table_of_summary_numbers_100913d1409.xlsx"

I'd like to show the Peptide intensity histogram for a young and old sample as well. (old; I did this)

For the old sample I'll choose the sample with an entropy of 7.335901881 (406971_top-GRP6_01182012_old.gpr)
"C:\Users\kurtw_000\Documents\kurt\storage\CIM Research Folder\DR\2013\9-26-13\old and young mice gpr files\summary\aged mouse Distribution 111513d0927.png"

For the young sample I'll choose the sample with an entropy of 7.075669091 (407167_bot-GRP2_01182012_young.gpr)
"C:\Users\kurtw_000\Documents\kurt\storage\CIM Research Folder\DR\2013\9-26-13\old and young mice gpr files\summary\young mouse Distribution 111513d0930.png"

axis settings: 1000 y by 200 and 20,000 x

Young and aged mouse peptide intensity histograms
"C:\Users\kurtw_000\Documents\kurt\storage\CIM Research Folder\DR\2013\9-26-13\old and young mice gpr files\summary\young and aged mouse distributions 11-15-13.svg"
"C:\Users\kurtw_000\Documents\kurt\storage\CIM Research Folder\DR\2013\9-26-13\old and young mice gpr files\summary\young and aged mouse distributions 11-15-13.png"
}
}
---</Mouse young and old>
---<Human young and old  (Changes with age in humans)>
Changes with age in humans
data and graphs
{

Heatmap of Measures for young and aged humans
-I redid the young aged analysis which defined young as <=25 and aged as >=50 rather than using 40 as the cutoff point.
-[data for old version of young aged analysis 03-14-2014d1446]

Analysis with more disparate ages
C:\Users\kurtw_000\Documents\kurt\storage\CIM Research Folder\DR\2014\03-12-2014d1433\young aged analysis

Box and dotplot of entropy for young and aged humans
"C:\Users\kurtw_000\Documents\kurt\storage\CIM Research Folder\DR\2014\03-12-2014d1433\young aged analysis\young aged dotplot.png"

Heatmap of measures for young and aged humans
"C:\Users\kurtw_000\Documents\kurt\storage\CIM Research Folder\DR\2014\03-12-2014d1433\young aged analysis\young aged dotplot formatted 03-17-2014d0940.png"

Statistical significance of measures comparing young and aged humans
"C:\Users\kurtw_000\Documents\kurt\storage\CIM Research Folder\DR\2014\03-12-2014d1433\young aged analysis\human normals of many ages 03-12-2014d1435.xlsx"

SVM weight of measures comparing young and aged humans
"C:\Users\kurtw_000\Documents\kurt\storage\CIM Research Folder\DR\2014\03-12-2014d1433\young aged analysis\human normals of many ages 03-12-2014d1435.xlsx"

Machine learning statistics for young and aged humans
"C:\Users\kurtw_000\Documents\kurt\storage\CIM Research Folder\DR\2014\03-12-2014d1433\young aged analysis\ml\Table of machine learning statistics 03-12-2014d1549.xlsx"

Machine learning statistics for Chinese and Indian nationality
"C:\Users\kurtw_000\Documents\kurt\storage\CIM Research Folder\DR\2013\11-2-13\human normals of many ages 11-2-13\corrected values\human normals of many ages 11-5-13d1510.xlsx"

-Specific Peptide Analysis with Aged Humans
--C:\Users\kurtw_000\Documents\kurt\storage\lgdata_DR\2014\01-16-2014d1422\selected young aged gprs\specific peptide analysis
--useful table with all samples all features for young and aged data
--- "C:\Users\kurtw_000\Documents\kurt\storage\lgdata_DR\2014\01-16-2014d1422\selected young aged gprs\all samples all features 01-17-2014d0907.xlsx"
--"C:\Users\kurtw_000\Documents\kurt\storage\lgdata_DR\2014\01-16-2014d1422\selected young aged gprs\specific peptide analysis more disparate ages\table of machine learning stats 03-14-2014d1352.xlsx"
}
---</Human young and old>
--Rank of Measures (Which metrics of the AbStat measures provide the most information about healthy and disease states?)
---"Sum of rank of measures by p-value"
---"C:\Users\kurtw_000\Documents\kurt\storage\CIM Research Folder\DR\2013\10-31-13\summaries of measures 10-31-13\Running Rank of Measures 10-31-13.xlsx"
--Range of Entropy (What is the typical range of entropy in healthy and disease states?)
---"C:\Users\kurtw_000\Documents\kurt\storage\CIM Research Folder\DR\2013\10-31-13\summaries of measures 10-31-13\Measures from many experiments combined 2.xlsx"
---"C:\Users\kurtw_000\Documents\kurt\storage\CIM Research Folder\DR\2013\10-31-13\summaries of measures 10-31-13\normal range graphs\box and dotplot n and d from four exp 2 03-13-2014d1641.png"

--<Quantitative analysis of the entropy measure>
{

---<Changes in entropy measure with removal of certain peptides> (aka Changes in entropy measure with removal of peptides
)(What is the characteristic of the peptides which contribute the most to the entropy measurement of AbStat?)
{
---Analyzing which types of peptides are most important to allow the entropy to distinguish between groups
"F:\kurt\storage\CIM Research Folder\DR\2013\10-31-13\important peptide analysis pre 10-31-13"

P-value vs peptides removed
-part B: "C:\Users\kurtw_000\Documents\kurt\storage\CIM Research Folder\DR\2013\10-31-13\important peptide analysis pre 10-31-13\graphs and diagrams\log10 5p51 to 5p52 peptides removed 10-30-13.svg"

P-value vs least significant peptides removed
-"C:\Users\kurtw_000\Documents\kurt\storage\CIM Research Folder\DR\2013\10-31-13\important peptide analysis pre 10-31-13\graphs and diagrams\log10 zero to six least significant removed 3.png"

P-value vs lowest intensity peptides removed
-"C:\Users\kurtw_000\Documents\kurt\storage\CIM Research Folder\DR\2013\10-31-13\important peptide analysis pre 10-31-13\graphs and diagrams\P-value vs lowest intensity peptides remved 2 02-14-2014d1212.png"

Heatmap of highest intensities as highest intensity features are removed
-"C:\Users\kurtw_000\Documents\kurt\storage\CIM Research Folder\DR\2013\10-31-13\important peptide analysis pre 10-31-13\spreadsheets\Cell Plot of highest intensities as highest intensity peptides are removed 2000 threshold.jrp"
-"C:\Users\kurtw_000\Documents\kurt\storage\CIM Research Folder\DR\2013\10-31-13\important peptide analysis pre 10-31-13\spreadsheets\Cell Plot of highest intensities as highest intensity peptides are removed.jrp"
-"C:\Users\kurtw_000\Documents\kurt\storage\CIM Research Folder\DR\2013\10-31-13\important peptide analysis pre 10-31-13\spreadsheets\Cell Plot of highest intensities as highest intensity peptides are removed.svg"

}
---<\Changes in entropy measure with removal of certain peptides>

---<Change in entropy with change in bin size>
{
-figures
P-value vs bin size from 1 to 500 bin size
P-value vs bin size from 500 to 60,000 bin size
--"C:\Users\kurtw_000\Documents\kurt\storage\CIM Research Folder\DR\2013\10-31-13\important peptide analysis pre 10-31-13\varied bin size\p-value between BC and ND vs bin size 02-19-2014d1653.xlsx"
}
---<\Change in entropy with change in bin size>

}

}
-</Results>

-Discussion
{
--AbStat Changes with Artificial Antibody Experiments
---Discussion of Mechanism
---Equation for Kd calculation
----"C:\Users\kurtw_000\Documents\kurt\storage\CIM Research Folder\DR\2013\12-7-13\Kd calculation 12-07-2013d1148.docx"
----see [antibody peptide kd info portal 10-26-13]
----[one to one binding model calculation for gfod and gp120 kd 12-09-2013d1343] <-Some results from Chris to determine the Kd of the gfod and gp120 antibodies
--Mouse vaccines and infections
--Human vaccination data
--Reduction in antibody repertoire complexity with lymphoma
--Mouse cancer progression data
--Human disease data
--Alzheimers data
--Changes with Age
---use for adjusting baseline to baseline of normals
---quantifying attempts to mitigate aging process
--Rank of Measures
--Range of measures
--Analysis of important peptides
--Potential to combine ABSTAT into single number
--Use
---Diagnosis
---Constant monitoring
---Collect and analyze later
---Metric for improving performance and correlation with lifestyles
---Displaying results to public
--Potential of ABSTAT with specific peptides for different diseases
--Prediction about old and young vaccine results
--Applying same analysis to other datasets
---brain scan data (distribution of numbers for number of connections each neuron has; sanity and insanity)
---RNA expression data (expression levels of all of the different transcripts)
---prosperity of a city
---other data
--Other Measures?
---Discussion of Kolmogorov complexity and meaningful patterns
--Prediction about immune system training
}
-</Discussion>

azim58wiki: