Question: Batch effect and DE using TCGA and my data
0
gravatar for thaisenayane
6 months ago by
thaisenayane0 wrote:

Hello,

I'm trying to perform a differential gene expression analysis using some TCGA data that I reprocessed and my data. However I'm worried about the batch effect.

Normally to perform deseq I use this:

dds <- DESeqDataSetFromHTSeqCount(sampleTable = d, directory = directory, design= ~ batch)
dds <- estimateSizeFactors(dds)
dds <- DESeq(dds)

and then to plot an remove the batch effect I use this:

vsd <- vst(dds)
plotPCA(vsd, "batch")
assay(vsd) <- limma::removeBatchEffect(assay(vsd), vsd$batch)
plotPCA(vsd, "batch")

my doubt is about to perform differential gene expression after removing this batch effect with limma, is there any way? or DeSeq itself do this when I put batch as design?

Thanks

Thaise

rna-seq R • 283 views
ADD COMMENTlink modified 6 months ago by swbarnes27.5k • written 6 months ago by thaisenayane0

Please use the formatting bar (especially the code option) to present your post better. You can use backticks for inline code (`text` becomes text), or select a chunk of text and use the highlighted button to format it as a code block. I've done it for you this time.
code_formatting

ADD REPLYlink written 6 months ago by RamRS26k
2
gravatar for swbarnes2
6 months ago by
swbarnes27.5k
United States
swbarnes27.5k wrote:

or DeSeq itself do this when I put batch as design?

Yes. Don't try to correct for it, just let DESeq take it into account when making its models. You can also incorporate the design when calculating the PCA plot.

ADD COMMENTlink written 6 months ago by swbarnes27.5k
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