[BioC] Beadarray Filtering by Probequality

[Mark Dunning]

Hi Will,

It looks as though you are using the Illumina Humanv4 package to do
your annotation, whereas the example code was written with the Humanv3
annotation. Are you trying to follow the vignette with your own data?

What is the length of the 'rem' vector and the dimensions of the
BSData.norm object? There might be some mismatch here;

> length(rem)
[1] 49576
> dim(exampleSummaryData.norm)
Features  Samples Channels
   49576       12        1

Regards,

Mark

On Sun, Aug 26, 2012 at 8:21 PM, Will [guest] <guest at bioconductor.org> wrote:
>
> 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))
> table(qual)
>   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
> Will
>
>  -- output of sessionInfo():
>
> R version 2.15.1 (2012-06-22)
> Platform: x86_64-unknown-linux-gnu (64-bit)
>
> locale:
>  [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
> [11] LC_MEASUREMENT=en_US.iso885915 LC_IDENTIFICATION=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
>>
>
>
> --
> Sent via the guest posting facility at bioconductor.org.
>
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