I'm getting the following error when running processSwathData on files from a HiScan run on the HumanHT-12 v4. I'm wondering whether it is due to the fact that this chip type results in 3 swath files (at least with our instrument) instead of one or two as previously discussed (http://article.gmane.org/gmane.science.biology.informatics.conductor/ 38045/match=processSwathData). I've posted an example data set (5719680020.tar.gz) on ftp://ftp2.cancerresearchuk.org/pub/beadarray/ per the post above. I deleted the tif files to reduce the file size, but I get the same error when the images are included. processSwathData(twoColour=FALSE, segmentHeight=1800, segmentWidth=15750) 5719680020_A Error in cbind(txtFileCoords, locsFileCoords[, c(1, 4:ncol(locsFileCoords))]) : number of rows of matrices must match (see arg 2) sessionInfo() R version 2.14.0 (2011-10-31) 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] grid stats graphics grDevices utils datasets methods [8] base other attached packages: [1] beadarray_2.4.1 ggplot2_0.8.9 proto_0.3-9.2 reshape_0.8.4 [5] plyr_1.6 Biobase_2.14.0 loaded via a namespace (and not attached): [1] AnnotationDbi_1.16.10 BeadDataPackR_1.6.0 DBI_0.2-5 [4] IRanges_1.12.5 limma_3.10.0 RSQLite_0.11.1

Dear Stephen, You are correct, beadarray is currently only designed to deal with two swaths. I haven't previously encountered any data that was split into three. I don't know if that's a property of the chip type or the machine, but I suspect the latter. Our swath data has all been generated on the iScan (rather than HiScan) machine. Thank you very much for posting your data, that's a big help. It would be really great if you could include the images too, as I try to use the images as a verification step in breaking the text file down into the component parts. I won't need an entire chip, but the three swaths from one array section would be great. I'm afraid I won't get a chance to look at this until the new year as I'm on holiday from tomorrow, but I shall let you know when I've made processSwathData() more generalisable over the number of swaths. Many thanks Mike Smith On Thu, Dec 22, 2011 at 7:55 PM, Stephen Edwards <swandle06@yahoo.com>wrote: > I'm getting the following error when running processSwathData on files > from a > HiScan run on the HumanHT-12 v4. I'm wondering whether it is due to the > fact > that this chip type results in 3 swath files (at least with our instrument) > instead of one or two as previously discussed > ( > http://article.gmane.org/gmane.science.biology.informatics.conductor /38045/match=processSwathData > ). > I've posted an example data set (5719680020.tar.gz) on > ftp://ftp2.cancerresearchuk.org/pub/beadarray/ per the post above. I > deleted > the tif files to reduce the file size, but I get the same error when the > images > are included. > > processSwathData(twoColour=FALSE, segmentHeight=1800, segmentWidth=15750) > 5719680020_A > Error in cbind(txtFileCoords, locsFileCoords[, c(1, > 4:ncol(locsFileCoords))]) : > number of rows of matrices must match (see arg 2) > sessionInfo() > R version 2.14.0 (2011-10-31) > 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] grid stats graphics grDevices utils datasets methods > [8] base > > other attached packages: > [1] beadarray_2.4.1 ggplot2_0.8.9 proto_0.3-9.2 reshape_0.8.4 > [5] plyr_1.6 Biobase_2.14.0 > > loaded via a namespace (and not attached): > [1] AnnotationDbi_1.16.10 BeadDataPackR_1.6.0 DBI_0.2-5 > [4] IRanges_1.12.5 limma_3.10.0 RSQLite_0.11.1 > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > -- Mike Smith PhD Student Computational Biology Group Cambridge University [[alternative HTML version deleted]]