problem for interpretation of resulted ComBat() plot
1
0
Entering edit mode
modarzi ▴ 10
@modarzi-16296
Last seen 4.0 years ago

HI, I ran ComBat() for batch effect correction in my TCGA RNA-seq. consequently, I have two choices for batch effect correction: Parametric and nonparametric adjustment. So, I have down Parametric adjustment and resulted plot available in this link. Now, I need to know should I apply nonparametric adjustment ComBat() on my data or not? I would like to know more about the interpretation of that plot.

I appreciate it if anybody shares his/her comment with me.

Best

ComBat sva batch effect RNA-seq • 1.1k views
ADD COMMENT
0
Entering edit mode
@w-evan-johnson-5447
Last seen 4 months ago
United States

The parametric approach should work just fine on your data. You are just looking for gross deviations from these distributions (bi-modal or extreme skewness). Your plots look good to me!

On Dec 6, 2019, at 11:25 AM, modarzi [bioc] <noreply@bioconductor.org<a rel="nofollow" href="mailto:noreply@bioconductor.org">noreply@bioconductor.org> wrote:

Activity on a post you are following on support.bioconductor.orghttps://support.bioconductor.org/

User modarzihttps://support.bioconductor.org/u/16296/ wrote Question: problem for interpretation of resulted ComBat() plothttps://support.bioconductor.org/p/126946/:

HI, I ran ComBat() for batch effect correction in my TCGA RNA-seq. consequently, I have two choices for batch effect correction: Parametric and nonparametric adjustment. So, I have down Parametric adjustment and resulted plot available in this linkhttps://www.dropbox.com/s/knay47rl9hxecib/Rplot_Combat_parametric%20adjustment_980818.bmp?dl=0. Now, I need to know should I apply nonparametric adjustment ComBat() on my data or not? I would like to know more about the interpretation of that plot.

I appreciate it if anybody shares his/her comment with me.

Best

ADD COMMENT

Login before adding your answer.

Traffic: 744 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6