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Richard Thompson
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10
@richard-thompson-5371
Last seen 10.0 years ago
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,arrayInf
oColNames=list(barcode=NULL,position="Sentrix_Position"),cdfName="huma
n1mv1c",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:
genomewidesnp6genomewidesnp5human370v1chuman370quadv3chuman550v3bhuman
650v3ahuman610quadv1bhuman660quadv1ahuman1mduov3bhumanomni1quadv1bhuma
nomniexpress12v1bhumanomni25quadv1bhumanimmuno12v1bhumancytosnp12v2p1h
..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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