[BioC] Beadarray Filtering by Probequality

Will [guest] guest at bioconductor.org
Sun Aug 26 21:21:11 CEST 2012

Hey all,

I have been following the BeadSummary tutorial for beadarray and when i get to the step where i filter out the probes that have a quality of "Bad" and "No Match" 

ids <- as.character(featureNames(BSData.norm)) 
qual <- unlist(mget(ids, illuminaHumanv4PROBEQUALITY, ifnotfound = NA))
  Bad        Good     Good***    Good****    No match     Perfect
      12376        1158         137         507         468       27335
 Perfect*** Perfect****
       2911        2394

rem <- qual == "No match" | qual == "Bad" | is.na(qual)
BSData.filt <- BSData.norm[!rem, ]

I get the following error

Error in FUN(X[[2L]], ...) : (subscript) logical subscript too long

I was wondering if any one can help me figure out what's going on or help me come up with an alternative to filter out the reads with poor probe quality

Thanks in advance 

 -- output of sessionInfo(): 

R version 2.15.1 (2012-06-22)
Platform: x86_64-unknown-linux-gnu (64-bit)

 [1] LC_CTYPE=en_US.iso885915       LC_NUMERIC=C
 [3] LC_TIME=en_US.iso885915        LC_COLLATE=en_US.iso885915
 [5] LC_MONETARY=en_US.iso885915    LC_MESSAGES=en_US.iso885915
 [7] LC_PAPER=C                     LC_NAME=C
 [9] LC_ADDRESS=C                   LC_TELEPHONE=C

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

other attached packages:
[1] illuminaHumanv4.db_1.14.0 org.Hs.eg.db_2.7.1
[3] RSQLite_0.11.1            DBI_0.2-5
[5] AnnotationDbi_1.18.1      beadarray_2.6.0
[7] ggplot2_0.9.1             Biobase_2.16.0
[9] BiocGenerics_0.2.0

loaded via a namespace (and not attached):
 [1] BeadDataPackR_1.8.0 colorspace_1.1-1    dichromat_1.2-4
 [4] digest_0.5.2        grid_2.15.1         IRanges_1.14.4
 [7] labeling_0.1        limma_3.12.1        MASS_7.3-18
[10] memoise_0.1         munsell_0.3         plyr_1.7.1
[13] proto_0.3-9.2       RColorBrewer_1.0-5  reshape2_1.2.1
[16] scales_0.2.1        stats4_2.15.1       stringr_0.6.1
[19] tools_2.15.1

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