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

[Ian B Stanaway]

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.