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DE heatmap before or after limma adjustment

Hi,

I have a proteomics data from MaxQuant software. According to the manual, the data has been normalized by the MaxQuant internal method. After cleanup, QC and imputation (imputation data), I have done the adjustment with limma for AOD, Sex and PMI (residual data). In the next step, I want to plot a DE heatmap for case and control. Which data should I use, the imputation data or residual data?

Thanks

heapmap limma de
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updated by Devon Ryan 10K • | written by boymin2020 8

1 answer

It would make the most sense to use the residual data, since otherwise the confounders will muddy the plot.

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written by Devon Ryan 10K

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