[BioC] PVAC and Affymetrix HuGene array

[James W. MacDonald]

Hi Tim,

On 11/26/2012 10:56 AM, Tim Van Damme wrote:
> Hello everyone
>
> I would like to use the pvac package to analyze data from Affymetrix HuGene 1.0 ST arrays. However, I keep getting this error when running the code:
>
>> raw<- ReadAffy(celfile.path="CELS")
>> library(pvac)
>> ft<- pvacFilter(raw)
> Making absent/present calls, preprocessing data ...
> Error in FUN(1:18[[1L]], ...) :
>    NA/NaN/Inf in foreign function call (arg 2)

This is because the function is trying to compute present/absent calls, 
which are based on a comparison between the PM and MM probes. Since the 
HuGene array is a PM-only chip, this fails. You might contact the 
maintainer directly and see if they are planning to make a package that 
works with the newer Affy arrays.

Best,

Jim


>> traceback()
> 8: .C("DetectionPValue", as.double(pms[, x]), as.double(mms[, x]),
>         as.character(pns), as.integer(length(mms[, x])), as.double(tau),
>         as.double(sat), dpval = double(length(unique.pns)), length(unique.pns),
>         PACKAGE = "affy")
> 7: FUN(1:18[[1L]], ...)
> 6: lapply(X = X, FUN = FUN, ...)
> 5: sapply(1:length(pms[1, ]), function(x) {
>         .C("DetectionPValue", as.double(pms[, x]), as.double(mms[,
>             x]), as.character(pns), as.integer(length(mms[, x])),
>             as.double(tau), as.double(sat), dpval = double(length(unique.pns)),
>             length(unique.pns), PACKAGE = "affy")$dpval
>     })
> 4: mas5calls.AffyBatch(object, ...)
> 3: mas5calls(abatch, verbose = FALSE)
> 2: mas5calls(abatch, verbose = FALSE)
> 1: pvacFilter(raw)
>> sessionInfo()
> R version 2.15.1 (2012-06-22)
> Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)
>
> locale:
> [1] nl_BE.UTF-8/nl_BE.UTF-8/nl_BE.UTF-8/C/nl_BE.UTF-8/nl_BE.UTF-8
>
> attached base packages:
> [1] grid      stats     graphics  grDevices utils     datasets  methods
> [8] base
>
> other attached packages:
>   [1] BiocInstaller_1.8.3    pvac_1.4.0             hgu133plus2cdf_2.10.0
>   [4] gplots_2.11.0          KernSmooth_2.23-8      caTools_1.13
>   [7] bitops_1.0-4.2         gdata_2.12.0           gtools_2.7.0
> [10] RColorBrewer_1.0-5     statmod_1.4.16         limma_3.12.3
> [13] farms_1.8.2            MASS_7.3-22            hugene10stv1cdf_2.10.0
> [16] AnnotationDbi_1.18.4   affy_1.34.0            Biobase_2.16.0
> [19] BiocGenerics_0.2.0
>
> loaded via a namespace (and not attached):
> [1] affyio_1.24.0         DBI_0.2-5             IRanges_1.14.4
> [4] preprocessCore_1.18.0 RSQLite_0.11.2        stats4_2.15.1
> [7] tools_2.15.1          zlibbioc_1.2.0
>
> Any suggestions?
>
> Kind regards
> Tim
> 	[[alternative HTML version deleted]]
>
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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