Dear Rebecca,

Would it be possible for you to give me access to the offending data?  I've
only had access to one chip in the three swath format before so it's quite
likely the code doesn't cope with all possible formats.



On 28 August 2013 21:49, Rebecca Tagett [guest] <guest@bioconductor.org>wrote:

>
> Hello,
> I am a graduate student at Wayne State Univ in Detroit.
> I am trying to run beadarray's processSwathData for HumanHT12v4, with 3
> swaths, and I am getting the error shown below.
> I looked at the R code for processSwathData, and it is intended to handle
> 3 swaths.
> The only think that I can think might be a problem is  that the "glocs"
> matrices have different lengths.
>
> > dim(glocs1)
> [1] 404892      2
> > dim(glocs2)
> [1] 451836      2
> > dim(glocs3)
> [1] 404892      2
>
> Thanks for your help.
> Rebecca
>
>
> library("beadarray")
> library("illuminaHumanv4.db")
>
> processSwathData(inputDir = "9257259099_data",
>     outputDir = "9257259099_qc",
>     twoColour=FALSE, textstring="_perBeadFile.txt",  segmentHeight=326,
> segmentWidth=397,
>     fullOutput=TRUE, newTextString="_perSwath.txt", verbose=TRUE)
>
>
> 9257259099_A
> Reading green locs1... green locs2... Done
> Combining files... Done
> Matching duplicate spots... Assigning duplicated spot not supported with 3
> swaths;
>  734735 beads cannot be assigned to a swath and will be ignored
> Overlapping region: Segment 0
> Error in swath1[(seg * (segmentHeight * s1Width) + 1):((seg + 1) *
> (segmentHeight *  :
>   subscript out of bounds
>
>
>  -- output of sessionInfo():
>
>
>
> > sessionInfo()
> R version 3.0.1 (2013-05-16)
> Platform: x86_64-unknown-linux-gnu (64-bit)
>
> locale:
>  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
>  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
>  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
>  [7] LC_PAPER=C                 LC_NAME=C
>  [9] LC_ADDRESS=C               LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] parallel  stats     graphics  grDevices utils     datasets  methods
> [8] base
>
> other attached packages:
> [1] illuminaHumanv4.db_1.18.0 org.Hs.eg.db_2.9.0
> [3] RSQLite_0.11.4            DBI_0.2-7
> [5] AnnotationDbi_1.22.6      beadarray_2.10.0
> [7] ggplot2_0.9.3.1           Biobase_2.20.1
> [9] BiocGenerics_0.6.0
>
> loaded via a namespace (and not attached):
>  [1] AnnotationForge_1.2.2 BeadDataPackR_1.12.0  colorspace_1.2-2
>  [4] dichromat_2.0-0       digest_0.6.3          grid_3.0.1
>  [7] gtable_0.1.2          IRanges_1.18.3        labeling_0.2
> [10] limma_3.16.7          MASS_7.3-28           munsell_0.4.2
> [13] plyr_1.8              proto_0.3-10          RColorBrewer_1.0-5
> [16] reshape2_1.2.2        scales_0.2.3          stats4_3.0.1
> [19] stringr_0.6.2
>
>
>
> --
> Sent via the guest posting facility at bioconductor.org.
>
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-- 
Mike Smith
Research Associate
Statistics & Computational Biology Laboratory
Cambridge University

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