Hi, I am still struggling with my first try at working with Illumina bead array expression data, specifically getting the data read by the R package beadarray. The data was created by an off-site collaborator using BeadStudio version 3.0.14. My collaborator sent two types of files to me: (1) a number of .csv files (read by excel, 2 for each sample) with columns Illumicode, N, mean GRN, Dev GRN. (2) a summary .txt file with columns TargetID MIN_Signal-1814647013_A AVG_Signal-1814647013_A MAX_Signal-1814647013_A NARRAYS-1814647013_A ARRAY_STDEV-1814647013_A BEAD_STDEV-1814647013_A Avg_NBEADS-1814647013_A Detection-1814647013_A, with the MIN_Signal-... to Detection-... columns repeated for the remaining samples. I read the summary data(2) with the statement readBeadSummaryData(dataFile, skip=8, columns = list(exprs = "AVG_Signal", BeadStDev = "BEAD_STDEV", NoBeads = "Avg_NBEADS"), sep="\t"), but every time I do this R gets hung up (no error message). I also tried reading the bead-level data (the .csv files) with the statement BLData <- readIllumina(textType = ".csv") but then I get the error message Error in strtrim(x, width) : invalid 'width' argument Any suggestions would be much appreciated. Thank you. Ina

Hi Ina, Sorry to hear you are having such a struggle reading in your Illumina data. I noticed a problem reading in BeadStudio 3 output a few weeks ago and checked in a fix to the developmental version of beadarray. So if you upgrade to the latest version of beadarray (1.5.8, available from http://bioconductor.org/packages/2.1/bioc/html/beadarray.html) your summary data should read in without incident. Note that the default arguments to readBeadSummaryData() have been set for BeadStudio 3 output, so all you need to set it the filename. I have also added some more meaningful warnings to readIllumina(), which will help diagnose the cause of the second error you mention (most likely you are missing the tiff files, so try useImages=FALSE). Best wishes, Matt > Hi, > I am still struggling with my first try at working with Illumina bead > array expression data, specifically getting the data read by the R > package beadarray. > > The data was created by an off-site collaborator using BeadStudio > version 3.0.14. My collaborator sent two types of files to me: > (1) a number of .csv files (read by excel, 2 for each sample) with > columns Illumicode, N, mean GRN, Dev GRN. > (2) a summary .txt file with columns TargetID > MIN_Signal-1814647013_A AVG_Signal-1814647013_A > MAX_Signal-1814647013_A NARRAYS-1814647013_A > ARRAY_STDEV-1814647013_A BEAD_STDEV-1814647013_A > Avg_NBEADS-1814647013_A Detection-1814647013_A, with the > MIN_Signal-... to Detection-... columns repeated for the remaining samples. > > I read the summary data(2) with the statement > readBeadSummaryData(dataFile, skip=8, columns = list(exprs = > "AVG_Signal", BeadStDev = "BEAD_STDEV", NoBeads = "Avg_NBEADS"), sep="\t"), > but every time I do this R gets hung up (no error message). > > I also tried reading the bead-level data (the .csv files) with the statement > BLData <- readIllumina(textType = ".csv") > but then I get the error message > Error in strtrim(x, width) : invalid 'width' argument > > Any suggestions would be much appreciated. > Thank you. > Ina

Hi Ina, You can try the lumiR function in the lumi package, which can automatically detect the BeadStudio versions. For example: X.lumi = lumiR(fileName) The latest version of lumi can be downloaded from: http://www.bioconductor.org/packages/2.1/bioc/html/lumi.html Pan On 8/14/07 5:00 AM, "bioconductor-request at stat.math.ethz.ch" <bioconductor-request at="" stat.math.ethz.ch=""> wrote: > Message: 5 > Date: Mon, 13 Aug 2007 10:46:24 -0400 > From: Ina Hoeschele <inah at="" vt.edu=""> > Subject: [BioC] Illumina bead arrays > To: bioconductor at stat.math.ethz.ch > Message-ID: <46C06EC0.6020109 at vt.edu> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > Hi, > I am still struggling with my first try at working with Illumina bead > array expression data, specifically getting the data read by the R > package beadarray. > > The data was created by an off-site collaborator using BeadStudio > version 3.0.14. My collaborator sent two types of files to me: > (1) a number of .csv files (read by excel, 2 for each sample) with > columns Illumicode, N, mean GRN, Dev GRN. > (2) a summary .txt file with columns TargetID > MIN_Signal-1814647013_A AVG_Signal-1814647013_A > MAX_Signal-1814647013_A NARRAYS-1814647013_A > ARRAY_STDEV-1814647013_A BEAD_STDEV-1814647013_A > Avg_NBEADS-1814647013_A Detection-1814647013_A, with the > MIN_Signal-... to Detection-... columns repeated for the remaining samples. > > I read the summary data(2) with the statement > readBeadSummaryData(dataFile, skip=8, columns = list(exprs = > "AVG_Signal", BeadStDev = "BEAD_STDEV", NoBeads = "Avg_NBEADS"), sep="\t"), > but every time I do this R gets hung up (no error message). > > I also tried reading the bead-level data (the .csv files) with the statement > BLData <- readIllumina(textType = ".csv") > but then I get the error message > Error in strtrim(x, width) : invalid 'width' argument > > Any suggestions would be much appreciated. > Thank you. > Ina >

Just wondering, does your data file contain 8 rows of header space? The standard seems to be 7 with the AVG_ headers in row 8 (you can check by opening in excel) so skip=7. If you want to look at the bead level data you require the TIFF files and the csv files. This is not the standard format given as it requires adjustments to the machine and hence has to be requested before the chips are read. It may be that they have only given you summary data, and hence why there are errors with trying to read at bead-level. Im in the processes of annalysing my own Illumina data, (which I agree, is difficult with not as much info out there yet) hope I can help! Regards Alice -----Original Message----- From: bioconductor-bounces@stat.math.ethz.ch [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Pan Du Sent: Wednesday, 15 August 2007 2:35 a.m. To: bioconductor at stat.math.ethz.ch Cc: Ina Hoeschele Subject: Re: [BioC] Illumina bead arrays Hi Ina, You can try the lumiR function in the lumi package, which can automatically detect the BeadStudio versions. For example: X.lumi = lumiR(fileName) The latest version of lumi can be downloaded from: http://www.bioconductor.org/packages/2.1/bioc/html/lumi.html Pan On 8/14/07 5:00 AM, "bioconductor-request at stat.math.ethz.ch" <bioconductor-request at="" stat.math.ethz.ch=""> wrote: > Message: 5 > Date: Mon, 13 Aug 2007 10:46:24 -0400 > From: Ina Hoeschele <inah at="" vt.edu=""> > Subject: [BioC] Illumina bead arrays > To: bioconductor at stat.math.ethz.ch > Message-ID: <46C06EC0.6020109 at vt.edu> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > Hi, > I am still struggling with my first try at working with Illumina > bead array expression data, specifically getting the data read by the > R package beadarray. > > The data was created by an off-site collaborator using BeadStudio > version 3.0.14. My collaborator sent two types of files to me: > (1) a number of .csv files (read by excel, 2 for each sample) with > columns Illumicode, N, mean GRN, Dev GRN. > (2) a summary .txt file with columns TargetID > MIN_Signal-1814647013_A AVG_Signal-1814647013_A > MAX_Signal-1814647013_A NARRAYS-1814647013_A > ARRAY_STDEV-1814647013_A BEAD_STDEV-1814647013_A > Avg_NBEADS-1814647013_A Detection-1814647013_A, with the > MIN_Signal-... to Detection-... columns repeated for the remaining samples. > > I read the summary data(2) with the statement > readBeadSummaryData(dataFile, skip=8, columns = list(exprs = > "AVG_Signal", BeadStDev = "BEAD_STDEV", NoBeads = "Avg_NBEADS"), > sep="\t"), but every time I do this R gets hung up (no error message). > > I also tried reading the bead-level data (the .csv files) with the > statement BLData <- readIllumina(textType = ".csv") but then I get the > error message Error in strtrim(x, width) : invalid 'width' argument > > Any suggestions would be much appreciated. > Thank you. > Ina > _______________________________________________ Bioconductor mailing list Bioconductor at stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor

Matt Ritchie wrote: > Hi Ina, > > What operating system are you using? If you are on Windows, I have built a > version of beadarray under R-2.5.1 and made it available at our institute's > anonymous ftp server: > > ftp://ftp.cancerresearchuk.org/pub/any/beadarray/beadarray_1.5.8.zip > login: anonymous > password: your email address > > Best wishes, > > Matt > > Matt, I downloaded this version but I am still getting an error message while reading the data, please see below. > readBeadSummaryData(dataFile, skip=7, columns = list(exprs = + "AVG_Signal", BeadStDev = "BEAD_STDEV", NoBeads = "Avg_NBEADS"), sep="\t") Error in scan(file, what, nmax, sep, dec, quote, skip, nlines, na.strings, : line 336 did not have 98 elements (when I look at line 336 it does not look any different from the other lines, this is the same error that I had before, I also changed skip to 8 but this does not help, it then complains about line 335). Many thanks, Ina >> Matt Ritchie wrote: >> >>> Hi Ina, >>> >>> Sorry to hear you are having such a struggle reading in your Illumina data. >>> I noticed a problem reading in BeadStudio 3 output a few weeks ago and >>> checked in a fix to the developmental version of beadarray. >>> >>> So if you upgrade to the latest version of beadarray (1.5.8, available from >>> http://bioconductor.org/packages/2.1/bioc/html/beadarray.html) >>> >> Matt, this version was built under R 2.6, but the latest R version that >> I have (and that I can find) is R.2.5.1 - after installing this package >> I am getting error messages after I load the package with >> library(beadarray): >> Error in loadNamespace(name) : there is no package called 'AnnotationDbi' >> In addition: Warning message: package 'beadarray' was built under R >> version 2.6.0 >> Error in as.environment(pos) : no item called "newtable" on the search list >> >> (I don't find the package 'AnnotationDbi' in the list of downloadable >> packages). >> >> Any suggestion? >> Many thanks, Ina >> >>> your summary >>> data should read in without incident. Note that the default arguments to >>> readBeadSummaryData() have been set for BeadStudio 3 output, so all you need >>> to set it the filename. >>> >>> I have also added some more meaningful warnings to readIllumina(), which >>> will help diagnose the cause of the second error you mention (most likely >>> you are missing the tiff files, so try useImages=FALSE). >>> >>> Best wishes, >>> >>> Matt >>> >>> >>> >>>> Hi, >>>> I am still struggling with my first try at working with Illumina bead >>>> array expression data, specifically getting the data read by the R >>>> package beadarray. >>>> >>>> The data was created by an off-site collaborator using BeadStudio >>>> version 3.0.14. My collaborator sent two types of files to me: >>>> (1) a number of .csv files (read by excel, 2 for each sample) with >>>> columns Illumicode, N, mean GRN, Dev GRN. >>>> (2) a summary .txt file with columns TargetID >>>> MIN_Signal-1814647013_A AVG_Signal-1814647013_A >>>> MAX_Signal-1814647013_A NARRAYS-1814647013_A >>>> ARRAY_STDEV-1814647013_A BEAD_STDEV-1814647013_A >>>> Avg_NBEADS-1814647013_A Detection-1814647013_A, with the >>>> MIN_Signal-... to Detection-... columns repeated for the remaining samples. >>>> >>>> I read the summary data(2) with the statement >>>> readBeadSummaryData(dataFile, skip=8, columns = list(exprs = >>>> "AVG_Signal", BeadStDev = "BEAD_STDEV", NoBeads = "Avg_NBEADS"), sep="\t"), >>>> but every time I do this R gets hung up (no error message). >>>> >>>> I also tried reading the bead-level data (the .csv files) with the statement >>>> BLData <- readIllumina(textType = ".csv") >>>> but then I get the error message >>>> Error in strtrim(x, width) : invalid 'width' argument >>>> >>>> Any suggestions would be much appreciated. >>>> Thank you. >>>> Ina >>>> >>>>

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