Hi Ian, you should look for version 1.26.2 in the next few days. b


2014-02-12 17:46 GMT-02:00 Ian B Stanaway <bard@uw.edu>:

> Many Thanks!
>
> On Wed, Feb 12, 2014 at 11:39 AM, Benilton Carvalho
> <beniltoncarvalho@gmail.com> wrote:
> > Ian, I'm working on a fix, which should be available in the next couple
> of
> > days. Benilton
> >
> > On Feb 12, 2014 4:25 PM, "Ian B Stanaway" <bard@uw.edu> wrote:
> >>
> >> Hi,
> >>
> >> I should also note that if I remove the hist and boxplot sections of
> >> the script if proceeds and calculates all the normalizations, design,
> >> contrast.matrix and outputs topTables just fine.  It seems the naming
> >> in the graphical functions underlying code is off.
> >>
> >> best,
> >>
> >> Ian
> >>
> >> On Tue, Feb 11, 2014 at 1:59 PM, Ian [guest] <guest@bioconductor.org>
> >> wrote:
> >> >
> >> > Hi,
> >> >
> >> > I am analyzing some rat arrays. I get this error:
> >> >
> >> > Error in validObject(.Object) :
> >> >   invalid class "GeneFeatureSet" object: featureNames differ between
> >> > assayData and featureData
> >> > Calls: hist ... assayData<- -> assayData<- -> .init_NChannelSet ->
> >> > validObject
> >> >
> >> > I am pretty sure my code is close to correct as I put together this
> >> > script to analyze the pd.rat230.2 arrays for another project and it
> worked
> >> > great.
> >> >
> >> > Now I have switched to a project that used the pd.ragene.1.0.st.v1
> >> > instead and now I am getting this error and am in need of figuring it
> out
> >> > again.
> >> >
> >> > Any pointers would be great.
> >> >
> >> > Thanks,
> >> >
> >> > Ian
> >> >
> >> >  -- output of sessionInfo():
> >> >
> >> >> datadir <- "in_vitro_rat"
> >> >> setwd(datadir)
> >> >>
> >> >> celFiles <- list.celfiles()
> >> >> exp_data <- read.celfiles(celFiles, pkgname="pd.ragene.1.0.st.v1")
> >> > Platform design info loaded.
> >> > Reading in : 10.CEL
> >> > Reading in : 11.CEL
> >> > Reading in : 12.CEL
> >> > Reading in : 13.CEL
> >> > Reading in : 14.CEL
> >> > Reading in : 15.CEL
> >> > Reading in : 16.CEL
> >> > Reading in : 17.CEL
> >> > Reading in : 18.CEL
> >> > Reading in : 19.CEL
> >> > Reading in : 1.CEL
> >> > Reading in : 20.CEL
> >> > Reading in : 21.CEL
> >> > Reading in : 22.CEL
> >> > Reading in : 23.CEL
> >> > Reading in : 24.CEL
> >> > Reading in : 2.CEL
> >> > Reading in : 3.CEL
> >> > Reading in : 4.CEL
> >> > Reading in : 5.CEL
> >> > Reading in : 6.CEL
> >> > Reading in : 7.CEL
> >> > Reading in : 8.CEL
> >> > Reading in : 9.CEL
> >> >> png(file="exp.hist.png",width = 500, height = 600, type = "cairo")
> >> >> hist(exp_data)
> >> > Error in validObject(.Object) :
> >> >   invalid class "GeneFeatureSet" object: featureNames differ between
> >> > assayData and featureData
> >> > Calls: hist ... assayData<- -> assayData<- -> .init_NChannelSet ->
> >> > validObject
> >> > Execution halted
> >> >
> >> >
> >> > --
> >> > Sent via the guest posting facility at bioconductor.org.
>

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