Other papers on sample sizes for microarrays

2015-01-13

azim58 - Other papers on sample sizes for microarrays

Sample size paper (from Tiger)
http://www.biomedcentral.com/content/pdf/1471-2105-11-48.pdf

* This paper compares several different models, and proposes a new
  model for estimating the number of arrays needed to obtain a certain
  FDR. These models require making the calculations with the data from a
  pilot experiment. I thought this paper made things a little more
  complicated than I would have liked.
* "C:\kurt\storage\CIM Research
  Folder\DR\2013\2-2-13\data_download\1046\Power (annotated) and sample
  size estimation in microarray studies.pdf"

False discovery rate, sensitivity and sample size for microarray studies
http://bioinformatics.oxfordjournals.org/content/21/13/3017.short
"C:\kurt\storage\CIM Research
Folder\DR\2013\2-2-13\data_download\1046\False (annotated) discovery rate
sensitivity and sample size for microarray studies.pdf"

A simple method for assessing sample sizes in microarray experiments
http://w09.biomedcentral.com/1471-2105/7/106
This paper describes some software that can be used to see what the false
discovery rate would be if there are a certain number of features (genes
or peptides) called significant and a certain sample size was used. Their
false discovery rate is the same as the power of the test. Their method
considers any dependence between features. Their software can be
downloaded here
http://www-stat-class.stanford.edu/~tibs/clickwrap/sam.html. The
evaluation version of their software is limited to 500 genes.

* This paper refers to two other papers that could be interesting: one
  that assumes independence and equal variance [5] (False discovery rate,
  sensitivity and sample size for microarray studies), and another that
  assumes independence, but uses pilot data to estimate the variance [7].
  o One could potentially argue that antibodies binding to the random
    peptides is independent. However, if two different random peptides
    have very similar sequences, then they should bind well to the same
    antibody so maybe they are not fully independent.

* "C:\kurt\storage\CIM Research
  Folder\DR\2013\2-2-13\data_download\1046\A simple (annotated) method
  for assessing sample sizes in microarray experiments.pdf"

Sample size determination in microarray experiments for class comparison
and prognostic classification
http://biostatistics.oxfordjournals.org/content/6/1/27.short

Sample size for detecting differentially expressed genes in microarray
experiments
http://www.biomedcentral.com/1471-2164/5/87/about/citations-biomedcentral

(this paper is a review)
DESIGN ISSUES FOR cDNA MICROARRAY EXPERIMENTS
http://jacques.van-helden.perso.luminy.univmed.fr/bioinformatics_introducto
ry_course/web_course/articles/microarrays/yang_nature_reviews_genetics_2002
.pdf
"C:\kurt\storage\CIM Research
Folder\DR\2013\2-2-13\data_download\1046\Design (annotated) issues for
cDNA microarray experiments.pdf"

Statistical tests for differential expression in cDNA microarray
experiments
http://www.biomedcentral.com/content/pdf/gb-2003-4-4-210.pdf

Sample size for gene expression microarray experiments
http://bioinformatics.oxfordjournals.org/content/21/8/1502.short

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