Getting less DE genes when incorporating all samples
0
0
Entering edit mode
7 months ago
shome ▴ 10

When I am using 18 samples, I am getting upregulated genes as 2 and downregulated genes as 0.

Now, when I remove four samples, I am getting upregulated genes as 2000 and downregulated genes as 1000, using DESEq2.

What should be the most appropriate way to deal with this?

RNA-seq differential-expression deseq2 • 473 views
ADD COMMENT
2
Entering edit mode

Well, what have you looked at? Are those 4 samples outliers in the PCA? Is there reason to think there is an experimental reason for them to be bad? Or are you artificially removing accurate, but inconvenient samples to get the desired results?

ADD REPLY
2
Entering edit mode

I totally agree with the above comments.

Also, see the following in the DESeq2 tutorial: If I have multiple groups, should I run all together or split into pairs of groups?

ADD REPLY
0
Entering edit mode

Generally, for diagnosis you need to show code, experimental design and diagnostic plots such as PCA and MA-plots. Without that it's hard.

ADD REPLY

Login before adding your answer.

Traffic: 1734 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6