[BioC] beadarray\'s processSwathData for HumanHT12v4, with 3 swaths

Rebecca Tagett [guest] guest at bioconductor.org
Wed Aug 28 22:49:17 CEST 2013

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.


processSwathData(inputDir = "9257259099_data",
    outputDir = "9257259099_qc",
    twoColour=FALSE, textstring="_perBeadFile.txt",  segmentHeight=326, segmentWidth=397,
    fullOutput=TRUE, newTextString="_perSwath.txt", verbose=TRUE)

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)

 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
 [7] LC_PAPER=C                 LC_NAME=C
 [9] LC_ADDRESS=C               LC_TELEPHONE=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

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