I am working on microarray data analysis. to find out DE gene i have use p value <0.05. now i want to go with Benjamini-Hochberg correction, for this i have use samr package in R. for filtering significant genes delta value must be given by users. plz suggest me range of delta value and also give information about what is q value? how it is useful for Differential expression analysis of gene?
The reason why you are correcting the p values is multiple testing. In microarray data there are around 20.000 genes, as rows. So you do 20.000 times testing whether the gene is significantly DE. When you set your p value to 0.05, 1000 genes (20000 * 0.05) are significantly differentially expressed by chance. To avoid getting false positives or type-1 error, you correct your p values. Corrected p-values are generally called adjusted p values and q value is p value which is adjusted for False Discovery Rate (FDR).
To do that in R, you do not need to use any extra package. Following function will do the same job.
p.adjust(p.values, method = "BH", n = length(p.values))