Hi Michael,
On Sat, Apr 20, 2013 at 12:18 AM, Michael Love
<michaelisaiahl...@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
_______________________________________________
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
