Question: GEO differential expression analysis
gravatar for yehchan57
4 weeks ago by
yehchan570 wrote:

ID translation and remove duplicated genes which different probes are mapped are routine procedure in differential expression analysis using GEO series. However, when I do differential expression first then translate ID and remove duplicated genes, the number of DEG exceeds the former. Why?

deg R geo • 98 views
ADD COMMENTlink modified 4 weeks ago by zephyr_falcon70 • written 4 weeks ago by yehchan570
gravatar for zephyr_falcon
4 weeks ago by
New York, USA
zephyr_falcon70 wrote:

That's probably because of multiple testing. If you perform DE analysis BEFORE removing duplicates, the number of genes used in DE analysis is larger than that of DE analysis AFTER removing duplicates, and it will end up with lower FDRs because there are more genes. And lower FDR can be leaded to more DE genes.

ADD COMMENTlink written 4 weeks ago by zephyr_falcon70
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