Observation weights in zinbwave and it's use in deseq
0
0
Entering edit mode
6 months ago
pkallurkar • 0

Hello,

I have patch-seq data (n = 16 samples). I am interested in using ZINB-WaVE along with DESeq2 to extract DE genes. I am comparing the results if I run DESeq2 only and ZINB-WaVE plus DESeq2. I don't see any difference if Observation weights = FALSE. The number of DE significant genes (p-adj < 0.01 and L2FC > 1.5) are 123 genes, for both the cases.

However, if I do set Observation weights = TRUE, the number of DE genes post-ZINB-WaVE plus DESeq2 goes up to 1515 genes. Can someone please explain how DESeq2 is using the observation weights for analysis?

Thanks in advance.

zinbwave data deseq • 293 views
ADD COMMENT
0
Entering edit mode

Hi, you may want to post on Bioconductor support: https://support.bioconductor.org/ When you do that, please link up the 2 questions with a comment. Thanks

ADD REPLY

Login before adding your answer.

Traffic: 2224 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