Question: DESEQ2 Batch effect
0
gravatar for sherajilir
4 weeks ago by
sherajilir0
sherajilir0 wrote:

Hello everyone,

I am analyzing coad-tcga dataset and there are two sequencing platforms used, illuminaHiseq and IlluminaGA. Is there a way to remove batch effects in DESeq2 package prior to differential expression or does the GLM remove it automatically (which i dont hink happens).

Thanks!

deseq2 batch • 87 views
ADD COMMENTlink modified 4 weeks ago by Michael Love23k • written 4 weeks ago by sherajilir0
Answer: DESEQ2 Batch effect
0
gravatar for Michael Love
4 weeks ago by
Michael Love23k
United States
Michael Love23k wrote:

Take a look at our vignette. There we have a section on multi-factor design which shows how to control for covariates.

https://bioconductor.org/packages/release/bioc/vignettes/DESeq2/inst/doc/DESeq2.html#multi-factor-designs

ADD COMMENTlink written 4 weeks ago by Michael Love23k

Thank you Michael for your prompt response. I did normalization and i'm getting an MA plot like this

https://drive.google.com/file/d/1QeCzKQcTR5A-Wx7kGU52MvhfEj-27eCH/view?usp=sharing

Do you think its acceptable? I have doubts because its not aligned to zero.

Thank you once again

ADD REPLYlink written 4 weeks ago by sherajilir0

Sorry for writting separately but just came to my mind to use shrinkage with apeglm package and got this

https://drive.google.com/file/d/1ygZ1n9J_3he0L5ecFRFRTIPJV6TRzmmE/view?usp=sharing

Now i think the problem is solved, though your feedback would be highly valuable.

Thanks again

ADD REPLYlink written 4 weeks ago by sherajilir0
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