Question

DESEQ2 Batch effect

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sherajilir • 0

@sherajilir-18567

Last seen 4.6 years ago

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 • 1.1k views

ADD COMMENT • link updated 5.8 years ago by Michael Love 43k • written 5.8 years ago by sherajilir • 0

score 0 · Answer 1 · 2019-03-19

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Michael Love 43k

@mikelove

Last seen 6 days ago

United States

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 COMMENT • link 5.8 years ago Michael Love 43k

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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 REPLY • link 5.8 years ago sherajilir • 0

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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 REPLY • link 5.8 years ago sherajilir • 0