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Question: how to handle missing data for SampleTable in DESeq2
0
gravatar for anpham
3.9 years ago by
anpham0
anpham0 wrote:

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. 

ADD COMMENTlink modified 28 days ago by g.wang20 • written 3.9 years ago by anpham0
Answer: how to handle missing data for SampleTable in DESeq2
0
gravatar for Michael Love
3.9 years ago by
Michael Love22k
United States
Michael Love22k wrote:
Hi, Unfortunately we don't have any support for inference on covariates with missing data. You'd have to remove those subjects.
ADD COMMENTlink modified 3.9 years ago • written 3.9 years ago by Michael Love22k
Answer: how to handle missing data for SampleTable in DESeq2
0
gravatar for g.wang2
28 days ago by
g.wang20
g.wang20 wrote:

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 COMMENTlink written 28 days ago by g.wang20

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 REPLYlink written 28 days ago by James W. MacDonald49k

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

Regards Guan

ADD REPLYlink written 28 days ago by g.wang20
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