problem for interpretation of resulted ComBat() plot
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modarzi ▴ 10
@modarzi-16296
Last seen 9 months 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 • 226 views
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@w-evan-johnson-5447
Last seen 15 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

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