Question: DE heatmap before or after limma adjustment
gravatar for boymin2020
9 months ago by
boymin202020 wrote:


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?


limma heapmap de • 340 views
ADD COMMENTlink modified 8 months ago by Devon Ryan89k • written 9 months ago by boymin202020
gravatar for Devon Ryan
8 months ago by
Devon Ryan89k
Freiburg, Germany
Devon Ryan89k wrote:

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

ADD COMMENTlink written 8 months ago by Devon Ryan89k
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