[Bioc-devel] DESeq2 and <misc>Tranformsation(s)

[Steve Lianoglou]

Hi Michael,

On Sat, Apr 20, 2013 at 12:18 AM, Michael Love
<michaelisaiahlove at gmail.com> wrote:
> hi Steve,
>
> Thanks. Can you send a minimal example of the error? I can provide an
> alternate formula without error:
>
>> dds <- makeExampleDESeqDataSet()
>> design(dds) <- formula(~ condition)
>> rld <- rlogTransformation(dds)

I'll see your `condition` and raise you a `treatment` :-)

=======================
R> set.seed(123)
R> library(DESeq2)
R> dds <- makeExampleDESeqDataSet()
R> colData(dds)$treatment <- factor(sample(c("x", "y"), ncol(dds),
replace=TRUE))
R> design(dds) <- formula(~ condition + treatment)

## Fails for rlogTransformation
R> dds.rlog <- rlogTransformation(dds)
gene-wise dispersion estimates
mean-dispersion relationship
final dispersion estimates
Error in SummarizedExperiment(assays = rlogData(object, samplesVector,  :
  error in evaluating the argument 'assays' in selecting a method for
function 'SummarizedExperiment': Error in
modelMatrixNames[match(convertNames$from, modelMatrixNames)] <-
convertNames$to :
  NAs are not allowed in subscripted assignments

## vst seems OK
R> dds.vst <- varianceStabilizingTransformation(dds)
gene-wise dispersion estimates
mean-dispersion relationship
final dispersion estimates
========================

I'm using DESeq2_1.0.7 on R-3.0.0

Thanks,
-steve

--
Steve Lianoglou
Computational Biologist
Department of Bioinformatics and Computational Biology
Genentech