[BioC] RNA-Seq, generate batch-free count matrix

Steve Lianoglou lianoglou.steve at gene.com
Sat Aug 2 00:02:40 CEST 2014

Sorry to resurrect a somehow old thread, but I wanted to kick the
tires on this and wanted to clarify the google-record for posterity
... so:

On Sun, Jul 20, 2014 at 5:18 PM, Gordon K Smyth <smyth at wehi.edu.au> wrote:
> On Mon, 21 Jul 2014, Gordon K Smyth wrote:
>>  logCPMc <- removeBatchEffect(y, batch)
> Should have written
>  logCPMc <- removeBatchEffect(y2, batch)

Shouldn't the correction actually be this?

R> lobCPMc <- removeBatchEffect(logCPM, batch)

Because in the code snippet `y2` is a DGEList dataset (of counts).

So, removing batch effects from soup to nuts:

## ------------------------------------------------
y <- DGEList(counts=counts)

## Filter non-expressed genes:
A <- aveLogCPM(y)
y2 <- y2[A>1,]

## Then normalize and compute log2 counts-per-million with an offset
y2 <- calcNormFactors(y2)
logCPM <- cpm(y2, log=TRUE, prior.count=5)

## Then remove batch correct:
logCPMc <- removeBatchEffect(logCPM, batch)
## ------------------------------------------------


Steve Lianoglou
Computational Biologist

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