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].
 * 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_introductory_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