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What version of beadarray are you using? You might need to update it to the latest version. To ensure you get prompt help your post needs to include the output of: sessionInfo() Cheers Alice > -----Original Message----- > From: bioconductor-bounces at stat.math.ethz.ch > [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of ssls sddd > Sent: Tuesday, 2 October 2007 2:43 p.m. > To: bioconductor at stat.math.ethz.ch > Subject: [BioC] About beadarray package > > Hello! I tried to read in data using the function > readBeadSummaryData() but I got the error message like: > > Error in `rownames<-`(`*tmp*`, value = c(41306L, 35002L, > 16863L, 12131L, : > attempt to set rownames on object with no dimensions > > > I tried the sample data called 'raw_data.csv' and got quite > similar error > message: > > Error in `rownames<-`(`*tmp*`, value = c(1L, 2L, 3L, 4L, 5L, > 6L, 7L, 8L, : > attempt to set rownames on object with no dimensions > > > can anyone suggest how to correct this? > > Thank you very much! > > Alex > > [[alternative HTML version deleted]] > > _______________________________________________ > 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 > P Think before you print This e-mail transmission and any attachments that accompany it may contain information that is privileged, confidential or otherwise exempt from disclosure under applicable law and is intended solely for the use of the individual(s) to whom it was intended to be addressed. If you have received this e-mail by mistake, or you are not the intended recipient, any disclosure, dissemination, distribution, copying or other use or retention of this communication or its substance is prohibited. If you have received this communication in error, please immediately reply to the author via e-mail that you received this message by mistake and also permanently delete the original and all copies of this e-mail and any attachments from your computer. Thank you.

What is the command you are using, and what do the first few lines of your data file look like? ________________________________ From: ssls sddd [mailto:ssls.sddd at gmail.com] Sent: Tuesday, 2 October 2007 4:01 p.m. To: Johnstone, Alice Cc: bioconductor at stat.math.ethz.ch Subject: Re: [BioC] About beadarray package The result of sessionInfo () reads as below. But I think it is up-to-date. Thanks! Alex > sessionInfo() R version 2.5.1 (2007-06-27) i386-pc-mingw32 locale: LC_COLLATE=English_United States.1252;LC_CTYPE=English_United States.1252;LC_MONETARY=English_United States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 attached base packages: [1] "grid" "tools" "stats" "graphics" "grDevices" "utils" [7] "datasets" "methods" "base" other attached packages: beadarray beadarraySNP quantsmooth lodplot quantreg SparseM "1.4.0" " 1.2.0" "1.2.0" "1.1" "4.10" "0.73" affy affyio geneplotter lattice annotate Biobase "1.14.2" " 1.4.1" "1.14.0" "0.15-11" "1.14.1" "1.14.1" limma "2.10.5" On 10/1/07, Johnstone, Alice <alice.johnstone at="" esr.cri.nz=""> wrote: What version of beadarray are you using? You might need to update it to the latest version. To ensure you get prompt help your post needs to include the output of: sessionInfo() Cheers Alice > -----Original Message----- > From: bioconductor-bounces at stat.math.ethz.ch > [mailto: bioconductor-bounces at stat.math.ethz.ch <mailto:bioconductor-bounces at="" stat.math.ethz.ch=""> ] On Behalf Of ssls sddd > Sent: Tuesday, 2 October 2007 2:43 p.m. > To: bioconductor at stat.math.ethz.ch > Subject: [BioC] About beadarray package > > Hello! I tried to read in data using the function > readBeadSummaryData() but I got the error message like: > > Error in `rownames<-`(`*tmp*`, value = c(41306L, 35002L, > 16863L, 12131L, : > attempt to set rownames on object with no dimensions > > > I tried the sample data called 'raw_data.csv' and got quite > similar error > message: > > Error in `rownames<-`(`*tmp*`, value = c(1L, 2L, 3L, 4L, 5L, > 6L, 7L, 8L, : > attempt to set rownames on object with no dimensions > > > can anyone suggest how to correct this? > > Thank you very much! > > Alex > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch <mailto: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 > P Think before you print This e-mail transmission and any attachments that accompany it may contain information that is privileged, confidential or otherwise exempt from disclosure under applicable law and is intended solely for the use of the individual(s) to whom it was intended to be addressed. If you have received this e-mail by mistake, or you are not the intended recipient, any disclosure, dissemination, distribution, copying or other use or retention of this communication or its substance is prohibited. If you have received this communication in error, please immediately reply to the author via e-mail that you received this message by mistake and also permanently delete the original and all copies of this e-mail and any attachments from your computer. Thank you.

Alex, Try adding in: sep="," To your readBeadSummaryData() command. I think this should work as the default separator for this command is "\t", but you are using a *.csv file. Cheers Alice ________________________________ From: ssls sddd [mailto:ssls.sddd at gmail.com] Sent: Tuesday, 2 October 2007 5:31 p.m. To: Johnstone, Alice Cc: bioconductor at stat.math.ethz.ch Subject: Re: [BioC] About beadarray package Hi Alice, I used: library(beadarray) dataFile = "RawData_bkg_092107_Beadarrays.csv" BSData <- readBeadSummaryData(dataFile, ProbeID="TargetID",skip=0,columns = list(exprs = "AVG_Signal", BeadStDev = "BEAD_STDEV",NoBeads = "Avg_NBEADS")) I have attached a snapshot of first few lines of data. Thanks for the help! Alex On 10/1/07, Johnstone, Alice < Alice.Johnstone at esr.cri.nz <mailto:alice.johnstone at="" esr.cri.nz=""> > wrote: What is the command you are using, and what do the first few lines of your data file look like? ________________________________ From: ssls sddd [mailto:ssls.sddd at gmail.com] Sent: Tuesday, 2 October 2007 4:01 p.m. To: Johnstone, Alice Cc: bioconductor at stat.math.ethz.ch Subject: Re: [BioC] About beadarray package The result of sessionInfo () reads as below. But I think it is up-to-date. Thanks! Alex > sessionInfo() R version 2.5.1 (2007-06-27) i386-pc-mingw32 locale: LC_COLLATE=English_United States.1252 ;LC_CTYPE=English_United States.1252;LC_MONETARY=English_United States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 attached base packages: [1] "grid" "tools" "stats" "graphics" "grDevices" "utils" [7] "datasets" "methods" "base" other attached packages: beadarray beadarraySNP quantsmooth lodplot quantreg SparseM "1.4.0" " 1.2.0" "1.2.0" "1.1" "4.10" "0.73" affy affyio geneplotter lattice annotate Biobase "1.14.2" " 1.4.1" "1.14.0" "0.15-11" "1.14.1" "1.14.1" limma "2.10.5" On 10/1/07, Johnstone, Alice <alice.johnstone at="" esr.cri.nz=""> wrote: What version of beadarray are you using? You might need to update it to the latest version. To ensure you get prompt help your post needs to include the output of: sessionInfo() Cheers Alice > -----Original Message----- > From: bioconductor-bounces at stat.math.ethz.ch > [mailto: bioconductor-bounces at stat.math.ethz.ch <mailto:bioconductor-bounces at="" stat.math.ethz.ch=""> ] On Behalf Of ssls sddd > Sent: Tuesday, 2 October 2007 2:43 p.m. > To: bioconductor at stat.math.ethz.ch > Subject: [BioC] About beadarray package > > Hello! I tried to read in data using the function > readBeadSummaryData() but I got the error message like: > > Error in `rownames<-`(`*tmp*`, value = c(41306L, 35002L, > 16863L, 12131L, : > attempt to set rownames on object with no dimensions > > > I tried the sample data called 'raw_data.csv' and got quite > similar error > message: > > Error in `rownames<-`(`*tmp*`, value = c(1L, 2L, 3L, 4L, 5L, > 6L, 7L, 8L, : > attempt to set rownames on object with no dimensions > > > can anyone suggest how to correct this? > > Thank you very much! > > Alex > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch <mailto:bioconductor at="" stat.math.ethz.ch="" <mailto: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 > P Think before you print This e-mail transmission and any attachments that accompany it may contain information that is privileged, confidential or otherwise exempt from disclosure under applicable law and is intended solely for the use of the individual(s) to whom it was intended to be addressed. If you have received this e-mail by mistake, or you are not the intended recipient, any disclosure, dissemination, distribution, copying or other use or retention of this communication or its substance is prohibited. If you have received this communication in error, please immediately reply to the author via e-mail that you received this message by mistake and also permanently delete the original and all copies of this e-mail and any attachments from your computer. Thank you.