Crlmm Package And Genotyping With Snp 5 Chips (Affy)
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12.2 years ago
Alizaid12 • 0

Hi

I'm trying to perform some analysis on SNP5 arrays (Affymetrix) and am running problems for performing genotyping commands.

My ultimate aim is to use the genotyping information to perform a subsequent crlmmCopyNumber step in my R code.

The analysis progresses smoothly until determining gender estimations and then it shows as error message.

Please advise!!

library(crlmm)
cdfName <- "genomewidesnp5"
celPath <- "input"
outDir <- "output"
Listfiles <- list.celfiles()
ocProbesets(50e3)
batch <- as.factor(rep("A",length(Listfiles)))
plate<-substr(basename(Listfiles),1,8)
library(ff)
cnSet <- genotype(filenames = Listfiles,
                  cdfName = "genomewidesnp5", batch = plate)


Loading required package:genomewidesnp5Crlmm
Welcome to genomewidesnp5Crlmmversion1.0.4
Loading annotations and mixtliure model parameters.
Initializing ff objects.
Instantiating CNSet container
Preprocessing 169 files.
Cloning A and B matrices to store
genotype calls and confidence scores.
Quantile normalizing nonpolymorphicmarkers
Processing nonpolymorphic probes for 169 files.
Calling 605453 SNPs for recalibration... 
Loading annotations.
Determining gender.
Error in nrow(theCenters) : subscript out of bounds

sessionInfo()
R version 2.13.0 (2011-04-13)
Platform: x86_64-redhat-linux-gnu (64-bit)

locale:
[1] LC_CTYPE=en_US.utf8       LC_NUMERIC=C             

[3] LC_TIME=en_US.utf8        LC_COLLATE=en_US.utf8    
[5] LC_MONETARY=C             LC_MESSAGES=en_US.utf8   
[7] LC_PAPER=en_US.utf8       LC_NAME=C                
[9] LC_ADDRESS=C              LC_TELEPHONE=C           
[11] LC_MEASUREMENT=en_US.utf8 LC_IDENTIFICATION=C      

attached base packages:
[1] tools     stats     graphics  grDevices utils     datasets  methods  
[8] base     

other attached packages:
[1] genomewidesnp5Crlmm_1.0.4 ff_2.2-2                 
[3] bit_1.1-7                 crlmm_1.10.0             
[5] oligoClasses_1.14.0       Biobase_2.12.2           

loaded via a namespace (and not attached):
[1] affyio_1.20.0         annotate_1.30.0       AnnotationDbi_1.14.1 
[4] Biostrings_2.20.1     DBI_0.2-5             ellipse_0.3-5        
[7] genefilter_1.34.0     IRanges_1.10.4        mvtnorm_0.9-9991     
[10] preprocessCore_1.14.0 RSQLite_0.9-4         splines_2.13.0       
[13] survival_2.36-9       xtable_1.5-6
snp microarray affymetrix • 3.1k views
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Edited for better formatting. Please indent code and output with 4 spaces.

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might want to try here: http://www.bioconductor.org/help/mailing-list/#bioconductor and update to the latest R (2.14) since there would be a newer crlmm 1.12.1 that might have fixed this

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