Question: DESEQ2 : When we merge technical replicates raw reads, do we need to divide by the number of technical replicates ?
0
gravatar for ZheFrench
2.4 years ago by
ZheFrench10
ZheFrench10 wrote:

Question is in the title.

I know there is a collapseReplicates function in DESEQ2. But I didn't succeed to use it so I did the sum up manually.

In the vignette , 

The purpose of this function is to sum up read counts from technical replicates to create an object with a single column of read counts for each sample

It doesn't say that they divide after sum up...I was wondering if i need to divide the raw counts by the number of technical replicates added because it will have an impact on the size factor ?

Thanks

deseq2 • 502 views
ADD COMMENTlink modified 2.4 years ago by Simon Anders3.5k • written 2.4 years ago by ZheFrench10
Answer: DESEQ2 : When we merge technical replicates raw reads, do we need to divide by t
2
gravatar for Simon Anders
2.4 years ago by
Simon Anders3.5k
Zentrum für Molekularbiologie, Universität Heidelberg
Simon Anders3.5k wrote:

No, you should not divide by the number of samples. 

And, of course, the size factor will go up, but that's the point of it: After merging several technical replicates, the resulting sample has a bigger size.

ADD COMMENTlink written 2.4 years ago by Simon Anders3.5k
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