[BioC] crlmm Illumina cdfName "human1mv1c" not valid

[Robert Scharpf]

Hi Richard, 

This is a bug.  I checked in a fix for release version 1.14.3.  Both of the following should evaluate to TRUE

crlmm:::isValidCdfName("human1mv1c")
crlmm:::isValidCdfName("human1mv1cCrlmm")

thanks-

Rob


On Jul 1, 2012, at 1:36 PM, Richard Thompson wrote:

> Hi Everyone,
> 
> I was really hoping someone could help me with this; I've tried 
> searching to no avail, however I apologise if something similar has been 
> discussed before.
> 
> I'm trying to use crlmm to carry out LOH and CNV analysis based on .idat 
> files created using the Illumina 1M bead chips.
> 
> I'm sure I've got it installed correctly (I'm new to Bioconductor, but 
> I've been using R for years) and I've double-checked all my steps, but I 
> can't seem to get past this problem. Under both my normal installation 
> and vanilla, when I run:
> 
> crlmmIlluminaV2(sampleSheet=samplesheet,arrayNames=arrayNames,arrayInfoColNames=list(barcode=NULL,position="Sentrix_Position"),cdfName="human1mv1c",saveDate=TRUE,returnParams=TRUE,path=".")
> 
> I'm getting:
> 
> Error in crlmmIlluminaV2(sampleSheet = samplesheet, arrayNames = 
> arrayNames,  :
>   cdfName not valid.  see validCdfNames
> In addition: Warning message:
> In isValidCdfName(cdfName) :
>   cdfName must be one of the following: 
> genomewidesnp6genomewidesnp5human370v1chuman370quadv3chuman550v3bhuman650v3ahuman610quadv1bhuman660quadv1ahuman1mduov3bhumanomni1quadv1bhumanomniexpress12v1bhumanomni25quadv1bhumanimmuno12v1bhumancytosnp12v2p1h
> 
> ..even though the reference states that it is valid for other functions. 
> Can anyone give me any suggestion why this may be happening and/or how I 
> can get this to work?
> 
> Many Thanks
> Richard Thompson
> 
>> sessionInfo()
> R version 2.15.0 (2012-03-30)
> Platform: x86_64-redhat-linux-gnu (64-bit)
> 
> locale:
>  [1] LC_CTYPE=en_GB.utf8       LC_NUMERIC=C
>  [3] LC_TIME=en_GB.utf8        LC_COLLATE=en_GB.utf8
>  [5] LC_MONETARY=en_GB.utf8    LC_MESSAGES=en_GB.utf8
>  [7] LC_PAPER=C                LC_NAME=C
>  [9] LC_ADDRESS=C              LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_GB.utf8 LC_IDENTIFICATION=C
> 
> attached base packages:
> [1] tools     stats     graphics  grDevices utils     datasets  methods
> [8] base
> 
> other attached packages:
> [1] cacheSweave_0.6-1   stashR_0.3-5        filehash_2.2-1
> [4] ff_2.2-7            bit_1.1-8           crlmm_1.14.2
> [7] oligoClasses_1.18.0
> 
> loaded via a namespace (and not attached):
>  [1] affyio_1.24.0         annotate_1.34.1       AnnotationDbi_1.18.1
>  [4] Biobase_2.16.0        BiocGenerics_0.2.0    BiocInstaller_1.4.7
>  [7] Biostrings_2.24.1     codetools_0.2-8       DBI_0.2-5
> [10] digest_0.5.2          ellipse_0.3-7         foreach_1.4.0
> [13] genefilter_1.38.0     grid_2.15.0           IRanges_1.14.3
> [16] iterators_1.0.6       lattice_0.20-6        mvtnorm_0.9-9992
> [19] preprocessCore_1.18.0 RSQLite_0.11.1        splines_2.15.0
> [22] stats4_2.15.0         survival_2.36-14      XML_3.9-4
> [25] xtable_1.7-0          zlibbioc_1.2.0
>> 
> 
> 
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> 
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