on which data type limma::removeBatchEffect can be applyed?
Entering edit mode
luca.s ▴ 40
Last seen 9 hours ago

Hi, we have RNAseq data that have been generated with different library preparation kits and need to be put together. I have learned that the best way to accomodate for this is including it as batch effect in the design formula of the DE packages (e.g. DESeq, edgeR). However, we would still need to batch correct the counts for additional analyses (e.g. PCA, clustering), and we were thinking on using limma::removeBatchEffect. Here comes the question: on which data can we use this function? Vst, rlog, log2CPM appear adequate, Is it so? Can we use it also on raw counts (e.g. those generated by RSEM), DESeq2 normalized counts, TPM, or the function expects a different kind of data? Do we need to log2 the counts/TPM before applying the function? Any advise against using counts treated with limma::removeBatchEffect for subsequent differential expression analysis using DEseq2 or edgeR? Sorry for these naive question and in case a duplicate question I was not able to find has been already answered before. Thank you in advance.

batch limma • 200 views
Entering edit mode
ATpoint ★ 2.4k
Last seen 13 minutes ago

Please read the function help which states that log-expression values should be used. vst and rlog are on log scale so that is fine, so is logcpm from edgeR. edgeR/DESeq2 expect raw counts, this is described in the manuals.


Login before adding your answer.

Traffic: 491 users visited in the last hour
Help About
Access RSS

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6