Hello, Can you share what is actually differential gene expression? identification of Up and Down regulated genes by using the statistical measure is reliable? or is any other methods available for to find differential gene expression? or any merits and demerits for finding differential gene expression by using statistical methods?
Significantly differentially expressed genes are genes that are shown with a statistical test to differ between groups. Usually an adjusted p-value is used (e.g., Benjamini-Hochberg corrected), and a cut off of 0.05 is taken (but this is arbitrary). For gene expression analysis, mostly limma is used (moderated t-statistics).
There are also other methods which don't use 'real' statistics such as ranking, but you (or I) don't see them that often.
Dear mathavanbioinfo, Here is a nice review about the concepts of gene expression analysis
In addition to the limma that b.nota suggests to you, there are softwares for non-programmer that you could use, like GeneE on broad institute and genepattern
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