information about revisions from Dr. Johnston on Ch. 1

2014-08-29

Some general points to keep in mind
-1. credit where samples are from
-2. credit who ran samples
-3. contrast to ims results
--"One could ask if you have array data why do entropy because you could look at specific signature.  Where would entropy be of value?" 
-"K: all thru change to reflect that the peptides do not have intensity" (basically change the term "peptide intensity"; What term is better? (fluorescence intensity))
-all through change "random peptide" to "non-natural sequence peptide"  (non-natural sequence (Kurt: lets use this term as it is more precise and less confusing)
-"K: I think you need to go back and change format for each section presented." (in the results)  "1) what is idea testing.  2) what was the ims data on comparing this set of samples.  eg, the ad from normal were separated.  3) after presenting data, conclude with what you conclude data means."

Document for tracking accepted revisions
-"C:\Users\kurtw_000\Documents\kurt\storage\CIM Research Folder\kwhittem\Dissertation revisions from others\revisions from dr johnston 01-06-2014d0953\Kurt Whittemore Dissertation doc for tracking accepted revisions 12-13-2013d1519.docx"
Second document with his revisions (original document from Dr. Johnston) (I'm pretty sure this also contains all the revisions from his first document)
-"C:\Users\kurtw_000\Documents\kurt\storage\CIM Research Folder\kwhittem\Dissertation revisions from others\revisions from dr johnston 01-06-2014d0953\second document\Kurt Whittemore Dissertation 12-13-2013d1519.docx"
--https://mail.google.com/mail/u/0/?ui=2&shva=1#search/rest+of+the+remarks/14365de599975484
First document with his revisions
-"C:\Users\kurtw_000\Documents\kurt\storage\CIM Research Folder\kwhittem\Dissertation revisions from others\revisions from dr johnston 01-06-2014d0953\first document\Kurt Whittemore Dissertation 12-13-2013d1519.docx"
--https://mail.google.com/mail/u/0/?ui=2&shva=1#search/i+did+not+quite+finish/14364e88490d282e

Short to do list
-address general points above
-change all heatmaps to remove the "scree plot"
-add legends to some heatmaps
-remake box and dotplot figures (com)
--"K: these are important figures.  They are not very clear and too small.  It is not clear what top panel represents.  More explanation needed.  Do not assume too much. "

azim58wiki: