Other papers on sample sizes for microarrays
2015-01-13azim58 - 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
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
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
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
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
"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