[BioC] simpleaffy() not recognizing cdf file

[James W. MacDonald]

On 9/24/2012 5:14 PM, SAIC [guest] wrote:
> Hi,
>
> I am trying to perform QC on a Mouse Gene 1.0 ST Array using simpleaffy(). However, simpleaffy is not recognizing the cdf file associated with the array. According to the instructions in the simpleaffy() vignette, the cdf file has been renamed to have an extension of .qcdef and has been placed in the R library folder.

I am approximately 100% sure that there are no instructions in the 
simpleaffy vignette that say to do that. Perhaps you can point to a page 
number that gave you this idea?

>
> When I set the qc environment using:
>
> setQCEnvironment("mogene10stv1cdf.qcdef", getwd())
>
> I receive no errors, but I am still unable to obtain any qc results. The working directory is set to the R library location where the .cdf file has been saved.
>
> I receive the following errors when I try to run qc() after setting the qc environment:
>
>> qcs<- qc(affyData)
> Error in setQCEnvironment(cdfn) :
>    Could not find array definition file ' mogene10stv1cdf.qcdef '. Simpleaffy does not know the QC parameters for this array type.
> See the package vignette for details about how to specify QC parameters manually.
>
> the cleancdfname() function does not work either. When I try this, I receive the following error:
>
>
>> cleancdfname(mogene10stv1cdf, addcdf = TRUE)
> Error in paste("invalid CDF name:", cdfname) :
>    environments cannot be coerced to other types
>
> I don't know what that means, especially since the setQCEnvironment() function worked.
>
> Any suggestions on how to get bioconductor to read the cdf file for this array?

The simpleaffy package isn't designed for the current generation of Affy 
chips. It assumes that the chip has MM probes, which isn't true for the 
random primer type chips.

There are only two packages designed for these chips - oligo and xps. 
Both have vignettes that provide helpful hints.

Best,

Jim


>
> I am using R version 2.15.1
>
> Thanks!
>
>
>
>   -- output of sessionInfo():
>
>> sessionInfo()
> R version 2.15.1 (2012-06-22)
> Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)
>
> locale:
> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] simpleaffy_2.32.0      gcrma_2.28.0           BiocInstaller_1.4.7    genefilter_1.38.0      mogene10stv1cdf_2.10.0 AnnotationDbi_1.18.3   affy_1.34.0            Biobase_2.16.0         BiocGenerics_0.2.0
>
> loaded via a namespace (and not attached):
>   [1] affyio_1.24.0         annotate_1.34.1       Biostrings_2.24.1     DBI_0.2-5             IRanges_1.14.4        preprocessCore_1.18.0 RSQLite_0.11.2        splines_2.15.1        stats4_2.15.1         survival_2.36-14      tools_2.15.1          XML_3.9-4
> [13] xtable_1.7-0          zlibbioc_1.2.0
> --
> Sent via the guest posting facility at bioconductor.org.
>
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-- 
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099