Question: Common differentially expressed genes between two cell lines
0
4 months ago by
bn33010
bn33010 wrote:

I am analysing an RNA-seq dataset with the below given design in DESeq2

Sample-- CellLine-- Treatment
S1 C1 DMSO
S2 C1 DMSO
S3 C1 Drug
S4 C1 Drug
S5 C2 DMSO
S6 C2 DMSO
S7 C2 Drug
S8 C2 Drug

While it was fairly straightforward to get results for Drug vs DMSO within cell lines. I also need to look into the effect of drug common across both the cell lines. I can see two ways of doing this:-

1. Take the intersection of up and down regulated genes from the individual Drug vs DMSO comparisons
2. Use my design as ~CellLine + Treatment and then extract results for Drug vs DMSO. This should in theory give me genes that are significantly up/down across both the cell lines.

The approach [2] should be more sensitive. However taking a look at plotCounts for some of the top significant genes quite a few genes seems to come up with ~similar counts in one of the cell lines and a significant change in the other. Albeit this happens mostly when counts are low in all samples but still this doesn't seem intuitive. Is this a correct way to get the results or should I stick to approach [1]

deseq2 • 105 views
modified 4 months ago by Michael Love24k • written 4 months ago by bn33010
Answer: Common differentially expressed genes between two cell lines
3
4 months ago by
Michael Love24k
United States
Michael Love24k wrote:

If you require it is DE in both cell lines, (1) is the better way to go.