Question: Taking surrogate variable into account before running PCA
0
gravatar for wamiqsaifi
21 months ago by
wamiqsaifi0
wamiqsaifi0 wrote:

I ran SVA to get surrogate variables. I want to visualise my data taking into consideration the surrogate variables. I came to know tha modifying the original expression matrix is not a good idea (https://www.biostars.org/p/121489/). How can I go about doing this?

batch effect svaseq sva • 848 views
ADD COMMENTlink modified 20 months ago by ivivek_ngs4.7k • written 21 months ago by wamiqsaifi0
1
gravatar for lessismore
20 months ago by
lessismore600
Mexico
lessismore600 wrote:

Refer to : Remove Surrogate Variables and Batch

ADD COMMENTlink written 20 months ago by lessismore600
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gravatar for ivivek_ngs
20 months ago by
ivivek_ngs4.7k
Seattle,WA, USA
ivivek_ngs4.7k wrote:

Take a look at this biostars post. I have already provided a code snippet and some explanation of how to proceed and what features of the SVs should be taken into account.

Hint: You find SVs and make a new expression matrix with information of SVs as a corrected one and then visualize it with a PCA plot. If you want to use SVs in your model matrix for DE testing then you have to use the initial mod and a new model to incorporate the confounders in your new model. However, test the SVs well as to not overfit.

ADD COMMENTlink modified 20 months ago • written 20 months ago by ivivek_ngs4.7k
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