Dear Mark, I've managed to get this working. I removed all relevant packages from my R library (e.g. AnnotationDbi, beadarray, BiocGenerics, illuminaHumanv4.db and org.Hs.eg.db) and downloaded afresh. I'd like to say thank you very much for your help and support. I'm extremely grateful for the time you have devoted to helping me with this problem. Best wishes, Darren New sessionInfo > sessionInfo() R version 2.15.3 (2013-03-01) Platform: x86_64-w64-mingw32/x64 (64-bit) locale: [1] LC_COLLATE=English_United Kingdom.1252 LC_CTYPE=English_United Kingdom.1252 LC_MONETARY=English_United Kingdom.1252 [4] LC_NUMERIC=C LC_TIME=English_United Kingdom.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] illuminaHumanv4.db_1.18.0 org.Hs.eg.db_2.9.0 RSQLite_0.11.2 DBI_0.2-5 AnnotationDbi_1.22.6 [6] beadarray_2.10.0 ggplot2_0.9.3.1 Biobase_2.18.0 BiocGenerics_0.6.0 loaded via a namespace (and not attached): [1] AnnotationForge_1.0.3 BeadDataPackR_1.10.0 colorspace_1.2-2 dichromat_2.0-0 digest_0.6.3 grid_2.15.3 [7] gtable_0.1.2 IRanges_1.16.6 labeling_0.1 limma_3.14.4 MASS_7.3-23 munsell_0.4 [13] parallel_2.15.3 plyr_1.8 proto_0.3-10 RColorBrewer_1.0-5 reshape2_1.2.2 scales_0.2.3 [19] stats4_2.15.3 stringr_0.6.2 Old sessionInfo > sessionInfo() R version 2.15.3 (2013-03-01) Platform: x86_64-w64-mingw32/x64 (64-bit) locale: [1] LC_COLLATE=English_United Kingdom.1252 LC_CTYPE=English_United Kingdom.1252 LC_MONETARY=English_United Kingdom.1252 [4] LC_NUMERIC=C LC_TIME=English_United Kingdom.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] illuminaHumanv4.db_1.16.0 org.Hs.eg.db_2.8.0 RSQLite_0.11.2 DBI_0.2-5 AnnotationDbi_1.20.7 [6] beadarray_2.8.1 ggplot2_0.9.3.1 Biobase_2.18.0 BiocGenerics_0.4.0 loaded via a namespace (and not attached): [1] AnnotationForge_1.0.3 BeadDataPackR_1.10.0 colorspace_1.2-2 dichromat_2.0-0 digest_0.6.3 grid_2.15.3 [7] gtable_0.1.2 IRanges_1.16.6 labeling_0.1 limma_3.14.4 MASS_7.3-23 munsell_0.4 [13] parallel_2.15.3 plyr_1.8 proto_0.3-10 RColorBrewer_1.0-5 reshape2_1.2.2 scales_0.2.3 [19] stats4_2.15.3 stringr_0.6.2 tools_2.15.3 -----Original Message----- From: bioconductor-bounces@r-project.org [mailto:bioconductor- bounces@r-project.org] On Behalf Of Darren Plant Sent: 06 June 2013 15:28 To: Mark Dunning Cc: bioconductor at stat.math.ethz.ch Subject: Re: [BioC] beadarray - combining swath files Dear Mark, This seems to work when i use the modified sampleSheet but not the correct sample sheet method. I'm flummoxed! Best wishes, Darren > getwd() [1] "D:/work/RAMS" > processSwathData(inputDir = "D:/work/RAMS/data/9259561003", outputDir > = "D:/work/RAMS/data/9259561003", twoColour=NULL, > textstring="_perBeadFile.txt", segmentHeight=326, segmentWidth=397, > fullOutput=TRUE, newTextString=".txt") 9259561003_A 9259561003_B 9259561003_C 9259561003_D 9259561003_E 9259561003_F 9259561003_G 9259561003_H 9259561003_I 9259561003_J 9259561003_K 9259561003_L > sampleSheetFile <- paste("data", "/sampleSheet.csv", sep = "") > readLines(sampleSheetFile) [1] "[Header],,," "Investigator Name,James Sellu,," "Project Name,RAMS Whole Genome Expression Profiling,," "Experiment Name,Chip 1,," [5] "Date,31/05/2013,," "[Data],,," "Sample_Name,Sample_Group,Sentrix_ID,Sentrix_Position" "RAMS06012,poor,9259561003,A" [9] "RAMS12038,good,9259561003,B" "RAMS12001,good,9259561003,C" "RAMS21004,poor,9259561003,D" "RAMS12039,poor,9259561003,E" [13] "RAMS12016,good,9259561003,F" "RAMS12032,good,9259561003,G" "RAMS12041,poor,9259561003,H" "RAMS15003,poor,9259561003,I" [17] "RAMS20020,good,9259561003,J" "RAMS20022,good,9259561003,K" "RAMS10025,poor,9259561003,L" > data <- readIllumina("D:/work/RAMS/data", sampleSheet = > sampleSheetFile, useImages = FALSE, illuminaAnnotation = "Humanv4") Sample Sheet D:\work\RAMS\data\sampleSheet.csv will be used to read the data Data for section 9259561003_A not found Data for section 9259561003_B not found Data for section 9259561003_C not found Data for section 9259561003_D not found Data for section 9259561003_E not found Data for section 9259561003_F not found Data for section 9259561003_G not found Data for section 9259561003_H not found Data for section 9259561003_I not found Data for section 9259561003_J not found Data for section 9259561003_K not found Data for section 9259561003_L not found Error in analyseDirectory(dir = x, sectionNames = as.character(dirs[[x]]), : No data found for the specified sections ####### AND > sampleSheetFile2 <- paste("data", "/sampleSheet2.csv", sep = "") > readLines(sampleSheetFile2) [1] "[Header],,," "Investigator Name,James Sellu,," "Project Name,RAMS Whole Genome Expression Profiling,," "Experiment Name,Chip 1,," [5] "Date,31/05/2013,," "[Data],,," "Sample_Name,Sample_Group,Sentrix_ID,Sentrix_Position" "RAMS06012,poor,9259561003,A-Swath1" [9] "RAMS12038,good,9259561003,B-Swath1" "RAMS12001,good,9259561003,C-Swath1" "RAMS21004,poor,9259561003,D-Swath1" "RAMS12039,poor,9259561003,E-Swath1" [13] "RAMS12016,good,9259561003,F-Swath1" "RAMS12032,good,9259561003,G-Swath1" "RAMS12041,poor,9259561003,H-Swath1" "RAMS15003,poor,9259561003,I-Swath1" [17] "RAMS20020,good,9259561003,J-Swath1" "RAMS20022,good,9259561003,K-Swath1" "RAMS10025,poor,9259561003,L-Swath1" "RAMS06012,poor,9259561003,A-Swath2" [21] "RAMS12038,good,9259561003,B-Swath2" "RAMS12001,good,9259561003,C-Swath2" "RAMS21004,poor,9259561003,D-Swath2" "RAMS12039,poor,9259561003,E-Swath2" [25] "RAMS12016,good,9259561003,F-Swath2" "RAMS12032,good,9259561003,G-Swath2" "RAMS12041,poor,9259561003,H-Swath2" "RAMS15003,poor,9259561003,I-Swath2" [29] "RAMS20020,good,9259561003,J-Swath2" "RAMS20022,good,9259561003,K-Swath2" "RAMS10025,poor,9259561003,L-Swath2" > data <- readIllumina("D:/work/RAMS/data",sampleSheet = > sampleSheetFile2, useImages = FALSE, illuminaAnnotation = "Humanv4") Sample Sheet D:\work\RAMS\data\sampleSheet2.csv will be used to read the data Processing section 9259561003_A-Swath1 Processing section 9259561003_A-Swath2 Processing section 9259561003_B-Swath1 Processing section 9259561003_B-Swath2 Processing section 9259561003_C-Swath1 Processing section 9259561003_C-Swath2 Processing section 9259561003_D-Swath1 Processing section 9259561003_D-Swath2 Processing section 9259561003_E-Swath1 Processing section 9259561003_E-Swath2 Processing section 9259561003_F-Swath1 Processing section 9259561003_F-Swath2 Processing section 9259561003_G-Swath1 Processing section 9259561003_G-Swath2 Processing section 9259561003_H-Swath1 Processing section 9259561003_H-Swath2 Processing section 9259561003_I-Swath1 Processing section 9259561003_I-Swath2 Processing section 9259561003_J-Swath1 Processing section 9259561003_J-Swath2 Processing section 9259561003_K-Swath1 Processing section 9259561003_K-Swath2 Processing section 9259561003_L-Swath1 Processing section 9259561003_L-Swath2 -----Original Message----- From: Mark Dunning [mailto:mark.dunning@gmail.com] Sent: 06 June 2013 14:22 To: Darren Plant Cc: bioconductor at stat.math.ethz.ch Subject: Re: [BioC] beadarray - combining swath files Hi Darren, I think this should work data <- readIllumina("D:/work/RAMS/data",sampleSheet = sampleSheetFile, useImages = FALSE, illuminaAnnotation = "Humanv4") it assumes that each chip is a sub-directory of the directory that you specify. So putting "9259561003" in the path isn't needed - it will be trying to read data from D:\work\RAMS\data\9259561003\9259561003 Hope it works this time! Mark On Thu, Jun 6, 2013 at 1:50 PM, Darren Plant <darren.plant at="" manchester.ac.uk=""> wrote: Dear Mark, I'm running commands from my base directory basedir<-"D:/work/RAMS" setwd(basedir) my sampleSheet and array data are in D:/work/RAMS/data/9259561003 I've also tried this with no luck. > sampleSheetFile <- paste("data/9259561003", "/sampleSheet.csv", sep = "") > readLines(sampleSheetFile) [1] "[Header],,," "Investigator Name,James Sellu,," "Project Name,RAMS Whole Genome Expression Profiling,," "Experiment Name,Chip 1,," [5] "Date,31/05/2013,," "[Data],,," "Sample_Name,Sample_Group,Sentrix_ID,Sentrix_Position" "RAMS06012,poor,9259561003,A" [9] "RAMS12038,good,9259561003,B" "RAMS12001,good,9259561003,C" "RAMS21004,poor,9259561003,D" "RAMS12039,poor,9259561003,E" [13] "RAMS12016,good,9259561003,F" "RAMS12032,good,9259561003,G" "RAMS12041,poor,9259561003,H" "RAMS15003,poor,9259561003,I" [17] "RAMS20020,good,9259561003,J" "RAMS20022,good,9259561003,K" "RAMS10025,poor,9259561003,L" > data <- readIllumina("data/9259561003", sampleSheet = sampleSheetFile, useImages = FALSE, illuminaAnnotation = "Humanv4") Sample Sheet D:\work\RAMS\data\9259561003\sampleSheet.csv will be used to read the data Error in analyseDirectory(dir = x, sectionNames = as.character(dirs[[x]]), : Directory does not exist. The only way i managed to get data into beadarray was after modifying the sampleSheet as i described earlier. Best wishes, Darren -----Original Message----- From: Mark Dunning [mailto:mark.dunning at gmail.com] Sent: 06 June 2013 13:38 To: Darren Plant Cc: bioconductor at stat.math.ethz.ch Subject: Re: [BioC] beadarray - combining swath files Hi Darren, What directory are you running that command from? Mark On Thu, Jun 6, 2013 at 1:15 PM, Darren Plant <darren.plant at="" manchester.ac.uk=""> wrote: Dear Mark, I tried this originally as i hadn't read that the sampleSheet would require modification in the documentation you provide. However, I couldn't get any data in to beadarray without changing the sample sheet (error below). Is there something fundamental that I'm doing wrong? Would it be possible for me to share a section array with you to see if you can use import/summarize at your end? Thank you for your continued support, this has been a real struggle for me. Best wishes, Darren > sampleSheetFile <- paste("data/9259561003", "/sampleSheet.csv", sep = "") > readLines(sampleSheetFile) [1] "[Header],,," [2] "Investigator Name,James Sellu,," [3] "Project Name,RAMS Whole Genome Expression Profiling,," [4] "Experiment Name,Chip 1,," [5] "Date,31/05/2013,," [6] "[Data],,," [7] "Sample_Name,Sample_Group,Sentrix_ID,Sentrix_Position" [8] "RAMS06012,poor,9259561003,A" [9] "RAMS12038,good,9259561003,B" [10] "RAMS12001,good,9259561003,C" [11] "RAMS21004,poor,9259561003,D" [12] "RAMS12039,poor,9259561003,E" [13] "RAMS12016,good,9259561003,F" [14] "RAMS12032,good,9259561003,G" [15] "RAMS12041,poor,9259561003,H" [16] "RAMS15003,poor,9259561003,I" [17] "RAMS20020,good,9259561003,J" [18] "RAMS20022,good,9259561003,K" [19] "RAMS10025,poor,9259561003,L" > data <- readIllumina("data", sampleSheet = sampleSheetFile, useImages = FALSE, illuminaAnnotation = "Humanv4") Sample Sheet /home/mdehsdp4/RAMS/data/9259561003/sampleSheet.csv will be used to read the data Data for section 9259561003_A not found Data for section 9259561003_B not found Data for section 9259561003_C not found Data for section 9259561003_D not found Data for section 9259561003_E not found Data for section 9259561003_F not found Data for section 9259561003_G not found Data for section 9259561003_H not found Data for section 9259561003_I not found Data for section 9259561003_J not found Data for section 9259561003_K not found Data for section 9259561003_L not found Error in analyseDirectory(dir = x, sectionNames = as.character(dirs[[x]]), : No data found for the specified sections -----Original Message----- From: Mark Dunning [mailto:mark.dunning at gmail.com] Sent: 06 June 2013 13:02 To: Darren Plant Cc: bioconductor at stat.math.ethz.ch Subject: Re: [BioC] beadarray - combining swath files Hi Darren, You don't need to include each swath as a separate line in the sample sheet. i.e. have 12 rows with the sentrix position as A to L. beadarray should be able to detect that there are two swathes per array. Hope this helps, Mark On Thu, Jun 6, 2013 at 9:11 AM, Darren Plant <darren.plant at="" manchester.ac.uk=""> wrote: Dear Mark, Please see below for a copy of the commands i used. Unfortunately I'm still getting the same problem following your suggestion. Best wishes, Darren > processSwathData(inputDir = "data/9259561003", outputDir = "data/9259561003", twoColour=NULL, textstring="_perBeadFile.txt", segmentHeight=326, segmentWidth=397, fullOutput=TRUE, newTextString="_Grn.txt") > sampleSheetFile <- paste("data/9259561003", "/sampleSheet.csv", sep = "") > readLines(sampleSheetFile) [1] "[Header],,," "Investigator Name,,," [3] "Project Name,RMS Whole Genome Expression Profiling,," "Experiment Name,,," [5] "Date,31/05/2013,," "[Data],,," [7] "Sample_Name,Sample_Group,Sentrix_ID,Sentrix_Position" "RAMS06012,poor,9259561003,A-Swath1_Grn" [9] "RM06012,poor,9259561003,A-Swath2_Grn" "RM12038,good,9259561003,B-Swath1_Grn" [11] "RM12038,good,9259561003,B-Swath2_Grn" "RM12001,good,9259561003,C-Swath1_Grn" [13] "RM12001,good,9259561003,C-Swath2_Grn" "RM21004,poor,9259561003,D-Swath1_Grn" [15] "RM21004,poor,9259561003,D-Swath2_Grn" "RM12039,poor,9259561003,E-Swath1_Grn" [17] "RM12039,poor,9259561003,E-Swath2_Grn" "RM12016,good,9259561003,F-Swath1_Grn" [19] "RM12016,good,9259561003,F-Swath2_Grn" "RM12032,good,9259561003,G-Swath1_Grn" [21] "RM12032,good,9259561003,G-Swath2_Grn" "RM12041,poor,9259561003,H-Swath1_Grn" [23] "RM12041,poor,9259561003,H-Swath2_Grn" "RM15003,poor,9259561003,I-Swath1_Grn" [25] "RM15003,poor,9259561003,I-Swath2_Grn" "RM20020,good,9259561003,J-Swath1_Grn" [27] "RM20020,good,9259561003,J-Swath2_Grn" "RM20022,good,9259561003,K-Swath1_Grn" [29] "RM20022,good,9259561003,K-Swath2_Grn" "RM10025,poor,9259561003,L-Swath1_Grn" [31] "RM10025,poor,9259561003,L-Swath2_Grn" > data <- readIllumina("data", sampleSheet = sampleSheetFile, useImages = FALSE, illuminaAnnotation = "Humanv4") Sample Sheet D:\work\RAMS\data\9259561003\sampleSheet.csv will be used to read the data Processing section 9259561003_A-Swath1_Grn Processing section 9259561003_A-Swath2_Grn Processing section 9259561003_B-Swath1_Grn Processing section 9259561003_B-Swath2_Grn Processing section 9259561003_C-Swath1_Grn Processing section 9259561003_C-Swath2_Grn Processing section 9259561003_D-Swath1_Grn Processing section 9259561003_D-Swath2_Grn Processing section 9259561003_E-Swath1_Grn Processing section 9259561003_E-Swath2_Grn Processing section 9259561003_F-Swath1_Grn Processing section 9259561003_F-Swath2_Grn Processing section 9259561003_G-Swath1_Grn Processing section 9259561003_G-Swath2_Grn Processing section 9259561003_H-Swath1_Grn Processing section 9259561003_H-Swath2_Grn Processing section 9259561003_I-Swath1_Grn Processing section 9259561003_I-Swath2_Grn Processing section 9259561003_J-Swath1_Grn Processing section 9259561003_J-Swath2_Grn Processing section 9259561003_K-Swath1_Grn Processing section 9259561003_K-Swath2_Grn Processing section 9259561003_L-Swath1_Grn Processing section 9259561003_L-Swath2_Grn datasumm <- summarize(data,useSampleFac=T,sampleFac=rep(1:12,each=2)) Finding list of unique probes in beadLevelData 48324 unique probeIDs found Number of unmapped probes removed: 217 Summarizing G channel Processing Array 1 Summarizing G channel Processing Array 2 Removing outliers Using exprFun Using varFun Summarizing G channel Processing Array 3 Summarizing G channel Processing Array 4 Removing outliers Using exprFun Using varFun Summarizing G channel Processing Array 5 Summarizing G channel Processing Array 6 Removing outliers Using exprFun Using varFun Summarizing G channel Processing Array 7 Summarizing G channel Processing Array 8 Removing outliers Using exprFun Using varFun Summarizing G channel Processing Array 9 Summarizing G channel Processing Array 10 Removing outliers Using exprFun Using varFun Summarizing G channel Processing Array 11 Summarizing G channel Processing Array 12 Removing outliers Using exprFun Using varFun Summarizing G channel Processing Array 13 Summarizing G channel Processing Array 14 Removing outliers Using exprFun Using varFun Summarizin! g G channel Processing Array 15 Summarizing G channel Processing Array 16 Removing outliers Using exprFun Using varFun Summarizing G channel Processing Array 17 Summarizing G channel Processing Array 18 Removing outliers Using exprFun Using varFun Summarizing G channel Processing Array 19 Summarizing G channel Processing Array 20 Removing outliers Using exprFun Using varFun Summarizing G channel Processing Array 21 Summarizing G channel Processing Array 22 Removing outliers Using exprFun Using varFun Summarizing G channel Processing Array 23 Summarizing G channel Processing Array 24 Removing outliers Using exprFun Using varFun Making summary object Annotating control probes using package illuminaHumanv4.db Version:1.16.0 Error in value[[3L]](cond) : row names supplied are of the wrong length AnnotatedDataFrame 'initialize' could not update varMetadata: perhaps pData and varMetadata are inconsistent? -----Original Message----- From: Mark Dunning [mailto:mark.dunning at gmail.com] Sent: 05 June 2013 15:45 To: Darren Plant Cc: bioconductor at stat.math.ethz.ch Subject: Re: [BioC] beadarray - combining swath files Hi Darren, I'm having a little trouble trying to reproduce the error. What commands did you use to generate the bead- level data? It seems to work for the data that I have. In the meantime, you can force beadarray to consolidate sections by using the sampleFac argument. The resulting object will then have all columns (samples). > bsd <- summarize(bld,useSampleFac=T,sampleFac=rep(1:12,each=2)) > bsd ExpressionSetIllumina (storageMode: list) assayData: 48107 features, 12 samples element names: exprs, se.exprs, nObservations protocolData: none phenoData rowNames: 8106854095_A 8106854095_B ... 8106854095_L (12 total) varLabels: sampleID SampleFac varMetadata: labelDescription featureData featureNames: ILMN_1802380 ILMN_1893287 ... ILMN_1806862 (48107 total) fvarLabels: ArrayAddressID IlluminaID Status fvarMetadata: labelDescription experimentData: use 'experimentData(object)' Annotation: Humanv4 QC Information Available Slots: QC Items: Date, Beadchip, ..., SampleGroup, numBeads sampleNames: 8106854095_A-Swath1, 8106854095_A-Swath2, ..., 8106854095_L-Swath1, 8106854095_L-Swath2 Please send me your code though. Regards, Mark On Wed, Jun 5, 2013 at 9:43 AM, Darren <darren.plant at="" manchester.ac.uk=""> wrote: Sunitha M <sunkorner at="" ...=""> writes: > > Dear all, > > I am trying to analyse Illumina beadarray data produced by iScan for the first time. This scanner saves each > array in two different tiff images. As a first step, I used ProcessSwathData() function that > deconvolutes the bead-level data and creates two files, swath1 and swath2 for the two tiff images. > However, in the subsequent step, i. e. readIllumina function these two files are treated as if they are > from two different arrays (although they belong to one array). Is there any parameter we can pass to the > readIllumina function to indicate that those two files belongs to one array. > > Any help in this regard is highly appreciated. > > Thanks > > Sunitha > > [[alternative HTML version deleted]] > > > Dear Sunitha, i hope you don't mind me joining in but i am faced with the same problem. There is no information on how to proceed with iScan data after ProcessSwathData() as far as i can see. Please let me know if you figure this out. I think others have used Illumina software to process the tiff files as an alternative. Best wishes, Darren > _______________________________________________ > Bioconductor mailing list > Bioconductor at ... > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor _______________________________________________ Bioconductor mailing list Bioconductor at r-project.org https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor _______________________________________________ Bioconductor mailing list Bioconductor at r-project.org https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor