I am trying to use beadarray to import Illumina iScan data but I seem to be missing some detail earlier in the process than others who have posted to this mailing list. I sent the University of Cambridge instructions http://www.compbio.group.cam.ac.uk/Resources/illumina/index.html to the group that created the data and I got the .tif, _perBeadFile.txt , Swath1_Grn.locs , Swath2_Grn.locs , and the Metrics.txt file back from them. I ran processSwathData(inputDir='7911747003',twoColour=F,fullOutput=T ,textstring="_perBeadFile.txt") which gave me the swath1.txt and swath2.txt files I expected. They look like this Code Grn GrnX GrnY Weight 10008 528 261.5272 28315.51 1 10008 541 855.4937 29410.51 1 10008 388 912.4988 18482.5 1 10008 500 1188.497 17681.5 1 10008 545 236.5013 14603.5 1 10008 424 341.505 4820.499 1 10008 573 400.0708 4815.309 1 10008 440 921.5268 2849.498 1 10008 617 1717.477 23031.51 0.5 10008 604 1660.978 14248.01 0.5 10008 583 2007.477 14506.5 0.5 10008 738 1939.5 7212.493 0.5 10010 100 1198.26 29319.64 1 10010 84 1197.688 29261.74 1 Then I ran: > Illumina.data <- readIllumina() (all defaults with working directory folder containing processSwathData output files 7911747003_A-Swath1.txt, 7911747003_A- Swath2.txt, 7911747003_B-Swath1.txt ...) and I got the error message: The specified sampleSheet c:\Users\craig\Desktop\Current Projects\Lama\Test\sampleSheet.csv was not found No sample sheet was specified. Trying to read all Illumina files inc:\Users\craig\Desktop\Current Projects\Lama\Test Error in analyseDirectory(dir = rootdir, sectionNames = sectionNames, : iScan data detected This must first be processed with the function processSwathData() In addition: Warning message: In normalizePath(path.expand(path), winslash, mustWork) : path[1]="sampleSheet.csv": The system cannot find the file specified Can anyone tell me what I am doing wrong and why readIllumina is still upset with me having iScan data? Secondly, will I have to make a sampleSheet.csv/targets file and what is the expected format for that? if necessary I can probably put together some of the data to reproduce the problem but I suspect I am just being dumb and missed some detail(it's my first time seeing Illumina data). Any help would be appreciated. Craig > sessionInfo() R version 2.15.0 (2012-03-30) Platform: x86_64-pc-mingw32/x64 (64-bit) locale: [1] LC_COLLATE=English_United States.1252 [2] LC_CTYPE=English_United States.1252 [3] LC_MONETARY=English_United States.1252 [4] LC_NUMERIC=C [5] LC_TIME=English_United States.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] beadarray_2.6.0 ggplot2_0.9.1 Biobase_2.16.0 BiocGenerics_0.2.0 loaded via a namespace (and not attached): [1] AnnotationDbi_1.18.1 BeadDataPackR_1.8.0 colorspace_1.1-1 [4] DBI_0.2-5 dichromat_1.2-4 digest_0.5.2 [7] grid_2.15.0 IRanges_1.14.3 labeling_0.1 [10] limma_3.12.0 MASS_7.3-18 memoise_0.1 [13] munsell_0.3 plyr_1.7.1 proto_0.3-9.2 [16] RColorBrewer_1.0-5 reshape2_1.2.1 RSQLite_0.11.1 [19] scales_0.2.1 stats4_2.15.0 stringr_0.6 [22] tools_2.15.0 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues [[alternative HTML version deleted]]