Question: DESeq2: Including known contaminant in the design model does not change PCA plot
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gravatar for nilssonp386
8 months ago by
nilssonp3860 wrote:

I have a data set of 51 samples over 4 different conditions, and I want to visualise the similarity between the groups. I have already identified a known blood contamination which affects 7 of the samples, and have added a column named "contamination", with the labels "yes" or "no".

However, when I include this term in the design matrix, it does not affect the appearance of the PCA plot. It looks the same as without the term, and the 7 samples are outliers in reference to the other samples of the same condition.

Code:

d.deseq <- DESeqDataSetFromMatrix(countData = raw_counts,
                                  colData = sample_data,
                                  design = ~ contamination + condition)

vsd <- vst(d.deseq, blind=FALSE)

pcaData <- plotPCA(vsd, intgroup=c("condition"), returnData = TRUE)
percentVar <- round(100 * attr(pcaData, "percentVar"))

p <- ggplot(pcaData, ...)

Thanks a lot for help with troubleshooting and/or other suggestion how to deal with the contamination.

deseq2 • 144 views
ADD COMMENTlink modified 8 months ago by Michael Love25k • written 8 months ago by nilssonp3860
Answer: DESeq2: Including known contaminant in the design model does not change PCA plot
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gravatar for Michael Love
8 months ago by
Michael Love25k
United States
Michael Love25k wrote:

A "frequently asked question":

https://bioconductor.org/packages/release/bioc/vignettes/DESeq2/inst/doc/DESeq2.html#why-after-vst-are-there-still-batches-in-the-pca-plot

ADD COMMENTlink written 8 months ago by Michael Love25k

Thank you, sorry I've missed that. Does this take the treatment condition into account when correcting the batch effects, or does the design have to be provided to the ┬┤removeBatchEffect┬┤ function? I've looked in to the limma documentation but they use other input objects to start with.

ADD REPLYlink written 8 months ago by nilssonp3860

You would just provide the batch variable to that function, not the full design.

ADD REPLYlink written 8 months ago by Michael Love25k
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