hi Sylvain,

fyi I'm cc-ing the list.

It appears that exp.ann might already have a column called sizeFactors. Can
you show me this column, if it exists?

thanks

Mike


On Fri, Mar 7, 2014 at 10:34 AM, Sylvain Foisy Ph. D. <
sylvain.foisy@diploide.net> wrote:

> Hi,
>
> Just updated my R-devel install and it works a-ok. One question however:
> when I create my DESeq object, I get this:
>
> > genex<-DESeqDataSetFromMatrix(
> + countData=exp.data,
> + colData=exp.ann,
> + design=~ celltype)
> > genex<-DESeq(genex)
> using pre-existing size factors
> estimating dispersions
> gene-wise dispersion estimates
> Error in .local(object, ...) :
>   first calculate size factors, add normalizationFactors, or set
> normalized=FALSE
> > genex<-estimateSizeFactors(genex)
> > genex<-DESeq(genex)
> using pre-existing size factors
> estimating dispersions
> gene-wise dispersion estimates
> mean-dispersion relationship
> final dispersion estimates
> fitting model and testing
> blah…blah…blah…
>
> Why do I need to use estimateSizeFactors first? According to the vignette,
> the DESeq function should do this step; btw, the version I used before did
> not need me to do this prior to run the DESeq() function.
>
> Best regards
>
> S
>
> On Mar 5, 2014, at 9:44 PM, Michael Love <michaelisaiahlove@gmail.com>
> wrote:
>
> > hi Sylvain,
> >
> > I committed version 1.3.45 today, which should be available in 1 day.
> Please let me know if this clears up the error.
> >
> > thanks,
> >
> > Mike
> >
> >
> > On Wed, Mar 5, 2014 at 1:13 PM, Sylvain Foisy Ph. D. <
> sylvain.foisy@diploide.net> wrote:
> > Hi Michael,
> >
> > Cool ;-) Thanks for the excellent work!!
> >
> > Best regards
> >
> > S
> >
> > On Mar 5, 2014, at 12:34 PM, Michael Love <michaelisaiahlove@gmail.com>
> wrote:
> >
> >> Hi Sylvain,
> >>
> >> Thanks for posting this bug.  I should be able to commit a simple
> change today, which fixes this.
> >>
> >> Mike
> >>
> >>
> >> On Wed, Mar 5, 2014 at 10:42 AM, Sylvain Foisy Ph. D. <
> sylvain.foisy@diploide.net> wrote:
> >> Hi,
> >>
> >> I used DEseq2 v. 1.3 under R-devel because I have many different values
> for my design (celltype) and it worked ok. I upgraded my libraries this
> morning (bad,bad,bad…) and now it is not working. Might this be a bug?
> >>
> >> > exp.data<-read.table("./count_table_by_gene.txt",header=T,row.names=1)
> >> > exp.ann<-read.table("./desc_colonnes.txt",header=T)
> >> > genex<-DESeqDataSetFromMatrix(
> >> + countData=exp.data,
> >> + colData=exp.ann,
> >> + design=~ celltype)
> >> > genex
> >> class: DESeqDataSet
> >> dim: 25192 103
> >> exptData(0):
> >> assays(1): counts
> >> rownames(25192): A1BG A1BG-AS1 ... ZZEF1 ZZZ3
> >> rowData metadata column names(0):
> >> colnames(103): 169377_LYMPHO_B_accepted_hits.bam
> >>   169377_celltype1_accepted_hits.bam ...
> 999046_celltype_m_accepted_hits.bam
> >>   999046_celltype_n_accepted_hits.bam
> >> colData names(2): sizeFactor celltype
> >> > genex<-DESeq(genex)
> >> using pre-existing size factors
> >> estimating dispersions
> >> gene-wise dispersion estimates
> >> Error in relevel.factor(coldata[[v]], as.character(coldata[[v]][idx])) :
> >>   'ref' must be of length one
> >>
> >> My count files were created using easyRNASeq-stable.
> >>
> >> Thanks in advance
> >>
> >> Sylvain
> >>
> >> _______________________________________________
> >> Bioconductor mailing list
> >> Bioconductor@r-project.org
> >> https://stat.ethz.ch/mailman/listinfo/bioconductor
> >> Search the archives:
> http://news.gmane.org/gmane.science.biology.informatics.conductor
> >>
> >
> >
>
>

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