how to handle missing data for SampleTable in DESeq2
2
0
Entering edit mode
anpham ▴ 30
@anpham-7402
Last seen 4.0 years ago

I have RNAseq data for human subjects and plan to do a differential gene expression analysis using DESeq2. The covariates I plan to use include sex, age, genotypic principal components, and substance use. However, I have missing data for principal components and substance use and would like to know how to code these missing data in the SampleTable. Can I put "." for missing data or would I have to take out the subjects with missing data? Thanks. 

deseq2 sample_table missing data • 1.7k views
ADD COMMENT
0
Entering edit mode
@mikelove
Last seen 18 hours ago
United States
Hi, Unfortunately we don't have any support for inference on covariates with missing data. You'd have to remove those subjects.
ADD COMMENT
0
Entering edit mode
g.wang2 • 0
@gwang2-19579
Last seen 7 months ago

Hello there,

I found this post tends to overlap with the question I'd like to ask, but not entirely. Therefore, adding the question here to this post:

There're some low quality RNA-seq data or some data looking dissimilar in the sample distance analysis from a couple of samples that need removal. The samples were collected before, during and after a treatment. The question is - should the problematic samples be excluded only or the entire subject data to be removed in DESeq2 analysis? Thanks.

Regards Guan

ADD COMMENT
0
Entering edit mode

If you have a question, start a new thread. Simply piggy-backing on some four year old thread that you think is similar enough isn't the way to go. In addition, don't use the Add Answer button to ask questions! That button is literally wrapped in instructions saying that you should only use it to answer a question, so why would you use it to ask another question?

ADD REPLY
0
Entering edit mode

I see, thanks for pointing these out. I've now started a new post asking the question.

Regards Guan

ADD REPLY

Login before adding your answer.

Traffic: 410 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