Question: Batch effect and DE using TCGA and my data
0
gravatar for thaisenayane
11 days 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 • 105 views
ADD COMMENTlink modified 11 days ago by swbarnes26.5k • written 11 days 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 11 days ago by RamRS24k
1
gravatar for swbarnes2
11 days ago by
swbarnes26.5k
United States
swbarnes26.5k 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 11 days ago by swbarnes26.5k
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