Question

Including batch effects in the differential expression of gene analysis

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amy16 • 0

@amy16-14425

Last seen 6.3 years ago

Hi,

I am performing differential expression of gene/transcript analysis using new tuxedo pipeline for the analysis (HISAT2, String tie and Ballgown). Some of the samples within the experiment were sequenced in different batches. Can you please advise me on which step should I include the batch effects term in the analysis?

Thanks in advance

-Amy

ballgown new tuxedo pipleine • 1.1k views

ADD COMMENT • link updated 6.2 years ago by James W. MacDonald 67k • written 6.3 years ago by amy16 • 0

score 0 · Answer 1 · 2018-09-19

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James W. MacDonald 67k

@james-w-macdonald-5106

Last seen 10 hours ago

United States

The only point in that pipeline at which you can include batch effects is in the linear modeling step using ballgown. The ballgown vignette seems to cover this reasonably well - have you read it?

ADD COMMENT • link 6.2 years ago James W. MacDonald 67k

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Hi James,

Thanks for your reply. I read ballgown vignette and my understanding is that it is possible to include the expected bath effect correction term in the stattest function and adjustvars argument.

Please advise me if my I've got my understanding right.

Thanks in advance

-Amy

ADD REPLY • link 6.2 years ago amy16 • 0