non-integer counts in DESeq2
1
0
Entering edit mode
warrena • 0
@warrena-16186
Last seen 6.4 years ago

I have PRO-seq data with the following conditions: untreated (time 0), vehicle, and treatment (3 replicates each, 4 time points for each vehicle/treatment combination). I would like to evaluate treatment effects as a function of time. I have done the following:

1. Divided the reads in each condition by the corresponding DEseq size factor

2. Subtracted the vehicle mean from the treatment values at the corresponding time point (assuming additive effects)

3. Subtracted the min over the whole expression matrix (new min = 0)

I would like to use DESeq2 for DEG analysis, but clearly cannot enter the matrix of interest as counts. Would rounding be reasonable? Are alternative approaches advised?

deseq2 differential gene expression • 1.9k views
ADD COMMENT
1
Entering edit mode
@mikelove
Last seen 1 day ago
United States

Do not use subtracted values as input to DESeq2 or any count method.

You can account for baseline values using interaction models, and keep the data on the original count scale. See the interaction section of the DESeq2 vignette.

ADD COMMENT

Login before adding your answer.

Traffic: 456 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