[BioC] Errors using particular 'Affy' package functions

[Vincent Carey]

have a look at

http://www.bioconductor.org/docs/workflows/oligoarrays/

you will find the entry

Affymetrix Gene ST Arrays

oligo

    * Requires a pdInfoPackage built using pdInfoBuilder
    * This package collates cdf, probe, annotation data together
    * These packages are available from Bioconductor via biocLite()

xps

    * Requires installation of ROOT
    * Uses data files from Affymetrix (.CDF, .PGF, .CLF, .CSV) directly

specifically, if you go the oligo route,
you will need pd.hugene.1.0.st.v1 so that oligo read.celfiles will
work for import

the resulting object can be processed with oligo::rma

you may also find hugene1.0stprobeset.db or
hugene1.0sttranscriptcluster.db packages
useful for annotation.  have a look at the ArrayTools package as well.

On Wed, Jul 29, 2009 at 5:55 AM, Cathrine
Mitchell<cathrine.mitchell at simugen-global.com> wrote:
> To whom it may concern,
>
> I am using R 2.9.1 in Linux (Ubuntu - Hardy). I have successfully installed
> 'affy' and it's dependencies.
> I am using a toy array dataset to make sure that I can analyse these arrays
> using affy.
> The data consists of 15 arrays (GeneChip Human Gene 1.0 ST Arrays).
> I have successfully read these arrays into my R workspace (I created the
> cdfpackage from the human gene st cdf file from affymetrix using
> makecdfenv):
>
>> Data
> AffyBatch object
> size of arrays=1050x1050 features (10 kb)
> cdf=hugenestcdf (33252 affyids)
> number of samples=15
> number of genes=33252
> annotation=hugenestcdf
> notes=
>
>
> I want to be able to create a boxplot and MAplot as described in the 'affy'
> primer pdf given on bioconductor (I am able to do this with the Dilution
> data provided on bioconductor) but when I try this on my 'Data' I get the
> following errors:
>
>> boxplot(Data)
> Error in data.frame(log2(intensity(x)[tmp, ])) :
>  row names contain missing values
> In addition: Warning message:
> In data.frame(log2(intensity(x)[tmp, ])) : NAs introduced by coercion
> Error in boxplot(data.frame(log2(intensity(x)[tmp, ])), main = main, range =
> range,  :
>  error in evaluating the argument 'x' in selecting a method for function
> 'boxplot'
>
>  > MAplot(Data)
> Error in .local(object, ...) : subscript out of bounds
> In addition: Warning message:
> In .local(object, ...) : NAs introduced by coercion
>
>
> When trying to fitPLM to the data I also get the following error:
>
>> library('affyPLM')
> Loading required package: gcrma
> Loading required package: matchprobes
> Loading required package: splines
> Loading required package: preprocessCore
>
> Attaching package: 'affyPLM'
>
>
>    The following object(s) are masked from package:stats :
>
>     resid,
>     residuals,
>     weights
>
>> plm.data <- fitPLM(Data)
> Error in .local(object, ...) : subscript out of bounds
> In addition: Warning message:
> In .local(object, ...) : NAs introduced by coercion
>
>
> I don't know what the errors mean or how to fix the problem so that I can
> analyse the data. Can 'affy' be used to analyse the Human Gene 1.0 ST array?
>
>
> Thank you very much
>
> Cathrine Mitchell
>
>        [[alternative HTML version deleted]]
>
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-- 
Vincent Carey, PhD
Biostatistics, Channing Lab
617 525 2265