[BioC] beadarray\'s processSwathData for HumanHT12v4, with 3 swaths
Rebecca Tagett [guest]
guest at bioconductor.org
Wed Aug 28 22:49:17 CEST 2013
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
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