[BioC] error with pd.ragene1.0.st.v1 and oligo

[Ian B Stanaway]

Many Thanks!

On Wed, Feb 12, 2014 at 11:39 AM, Benilton Carvalho
<beniltoncarvalho at 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 at 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 at 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.