beadarray\'s processSwathData for HumanHT12v4, with 3 swaths
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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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