Can DEseq2 handle zero values for some genes?
1
0
Entering edit mode
raya.fai ▴ 60
@rayafai-9396
Last seen 12 months ago
Israel

Hi,

I wanted to ask if DEseq2 can handle zeros for some of the gene counts? 

Is it better to add 1 to all the gene counts and that way not have zeros at all for better anaylsis?

Thank you very much,

Raya

 

deseq2 • 2.3k views
ADD COMMENT
0
Entering edit mode

Thank you very much.

Can I use DEseq2 if about 50% of the genes have zero counts in some of the replicates?

Thanks again,

Raya

ADD REPLY
0
Entering edit mode

I moved your post from an "Answer" to a "Comment".

The number of zeros itself is not an issue. You can use the plotSparsity() function to make a useful plot. What you don't want is to have the majority of genes with moderately high total counts (e.g. > 1000 sum of counts across samples) where a single sample makes up 99% of the total count. You should generally provide more information when you post a question, e.g. how many samples you have, what kind of comparison you want to make, is this typical bulk RNA-seq or some other experiment. Otherwise it's difficult to give more precise answers.

ADD REPLY
0
Entering edit mode

Thank you very much. Your answer was very helpful. I will try next time to ask more detailed questions.

Raya

ADD REPLY
0
Entering edit mode
@mikelove
Last seen 4 hours ago
United States

DESeq2 handles zeros as part of its model. You should not add a pseudocount.

 

ADD COMMENT

Login before adding your answer.

Traffic: 303 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