Hello all, I would like to be able to specify the sampleNames parameter to ReadAffy to ease later parsing and analysis of the data somewhat. The documentation (Textual description of affy vignete and ?ReadAffy) indicates that I need to set up a character array with both the file-names and the desired sample- names. This is what I have used (limited data-set for testing): > samples.files <- c( "RAE230A_043003_IM01T_LH.CEL", "RAE230A_043003_IM02T_LH.CEL", "RAE230A_043003_IM03T_LH.CEL", "RAE230A_043003_IM04T_LH.CEL", ); > samples.names <- c( "LET", "LEC", "WWT", "WWC", ); > Data <- ReadAffy( filenames = samples.files); sampleNames = samples.animals, ); But this fails with the error: Error in sub(pattern, replacement, x, ignore.case, extended) : invalid argument In addition: Warning message: sampleNames not same length as filenames. Using filenames as sampleNames instead in: ReadAffy(filenames = samples.files, sampleNames = samples.animals, So I tested: > length(samples.files); [1] 4 > length(samples.names); [1] 4 Have I misunderstood the purpose of the sampleNames argument? Or ss there another way of changing the "column" names in an eSet and in write.exprs() output? Any suggestions much appreciated! Paul ---------------------------------------- This mail sent through www.mywaterloo.ca

On Fri, 4 Jul 2003, Paul Boutros wrote: > Hello all, > > I would like to be able to specify the sampleNames parameter to ReadAffy to > ease later parsing and analysis of the data somewhat. The documentation > (Textual description of affy vignete and ?ReadAffy) indicates that I need to > set up a character array with both the file-names and the desired sample- > names. This is what I have used (limited data-set for testing): > > > samples.files <- c( > "RAE230A_043003_IM01T_LH.CEL", > "RAE230A_043003_IM02T_LH.CEL", > "RAE230A_043003_IM03T_LH.CEL", > "RAE230A_043003_IM04T_LH.CEL", > ); > > > samples.names <- c( > "LET", > "LEC", > "WWT", > "WWC", > ); > > > Data <- ReadAffy( > filenames = samples.files); > sampleNames = samples.animals, > ); > i don't get this error. make sure you syntax is correct. i usueally get this error when i forget to type filenmaes in ReadAffy(filenames=file.names), like this: ReadAffy(file.names). and are you sure you want samples.animals? in looking at this i found that ReadAffy (via read.affybatch) has a bug. it ignores the sampleNames argument. this bug has been fixed and should appear in release version 1.2.30 and devel version 1.3.5. in the meantime you can try not using the sampleNames argument and later use colnames(exprs(Data)) <- sample.names rownames(pData(Data)) <- sample.names > But this fails with the error: > > Error in sub(pattern, replacement, x, ignore.case, extended) : > invalid argument > In addition: Warning message: > sampleNames not same length as filenames. Using filenames as sampleNames instead > in: ReadAffy(filenames = samples.files, sampleNames = samples.animals, > > So I tested: > > length(samples.files); > [1] 4 > > length(samples.names); > [1] 4 > > Have I misunderstood the purpose of the sampleNames argument? Or ss there > another way of changing the "column" names in an eSet and in write.exprs() > output? > > Any suggestions much appreciated! > Paul > > ---------------------------------------- > This mail sent through www.mywaterloo.ca > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor >

Is it a typo in your email or did you really do the following: samples.names <- c( "LET", "LEC", "WWT", "WWC", ) Data <- ReadAffy( filenames = samples.files); sampleNames = samples.animals, ) If so, try changing sampleNames=samples.animals to sampleNames=samples.names. Jim James W. MacDonald UMCCC Microarray Core Facility 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623 >>> ririzarr@jhsph.edu 07/05/03 02:19AM >>> On Fri, 4 Jul 2003, Paul Boutros wrote: > Hello all, > > I would like to be able to specify the sampleNames parameter to ReadAffy to > ease later parsing and analysis of the data somewhat. The documentation > (Textual description of affy vignete and ?ReadAffy) indicates that I need to > set up a character array with both the file-names and the desired sample- > names. This is what I have used (limited data-set for testing): > > > samples.files <- c( > "RAE230A_043003_IM01T_LH.CEL", > "RAE230A_043003_IM02T_LH.CEL", > "RAE230A_043003_IM03T_LH.CEL", > "RAE230A_043003_IM04T_LH.CEL", > ); > > > samples.names <- c( > "LET", > "LEC", > "WWT", > "WWC", > ); > > > Data <- ReadAffy( > filenames = samples.files); > sampleNames = samples.animals, > ); > i don't get this error. make sure you syntax is correct. i usueally get this error when i forget to type filenmaes in ReadAffy(filenames=file.names), like this: ReadAffy(file.names). and are you sure you want samples.animals? in looking at this i found that ReadAffy (via read.affybatch) has a bug. it ignores the sampleNames argument. this bug has been fixed and should appear in release version 1.2.30 and devel version 1.3.5. in the meantime you can try not using the sampleNames argument and later use colnames(exprs(Data)) <- sample.names rownames(pData(Data)) <- sample.names > But this fails with the error: > > Error in sub(pattern, replacement, x, ignore.case, extended) : > invalid argument > In addition: Warning message: > sampleNames not same length as filenames. Using filenames as sampleNames instead > in: ReadAffy(filenames = samples.files, sampleNames = samples.animals, > > So I tested: > > length(samples.files); > [1] 4 > > length(samples.names); > [1] 4 > > Have I misunderstood the purpose of the sampleNames argument? Or ss there > another way of changing the "column" names in an eSet and in write.exprs() > output? > > Any suggestions much appreciated! > Paul > > ---------------------------------------- > This mail sent through www.mywaterloo.ca > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor > _______________________________________________ Bioconductor mailing list Bioconductor@stat.math.ethz.ch https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor

Rafael pointed out that there was a typo in my example. The correct version is below: > samples.files <- c( "RAE230A_043003_IM01T_LH.CEL", "RAE230A_043003_IM02T_LH.CEL", "RAE230A_043003_IM03T_LH.CEL", "RAE230A_043003_IM04T_LH.CEL", ); > samples.names <- c( "LET", "LEC", "WWT", "WWC", ); > Data <- ReadAffy( filenames = samples.files, sampleNames = samples.names ); > -----Original Message----- > From: Paul Boutros [mailto:pcboutro@engmail.uwaterloo.ca] > Sent: Friday, July 04, 2003 5:37 PM > To: bioconductor@stat.math.ethz.ch > Subject: Specifying Sample Names in ReadAffy; > > > Hello all, > > I would like to be able to specify the sampleNames parameter to > ReadAffy to > ease later parsing and analysis of the data somewhat. The documentation > (Textual description of affy vignete and ?ReadAffy) indicates > that I need to > set up a character array with both the file-names and the desired sample- > names. This is what I have used (limited data-set for testing): > > > samples.files <- c( > "RAE230A_043003_IM01T_LH.CEL", > "RAE230A_043003_IM02T_LH.CEL", > "RAE230A_043003_IM03T_LH.CEL", > "RAE230A_043003_IM04T_LH.CEL", > ); > > > samples.names <- c( > "LET", > "LEC", > "WWT", > "WWC", > ); > > > Data <- ReadAffy( > filenames = samples.files); > sampleNames = samples.animals, > ); > > But this fails with the error: > > Error in sub(pattern, replacement, x, ignore.case, extended) : > invalid argument > In addition: Warning message: > sampleNames not same length as filenames. Using filenames as > sampleNames instead > in: ReadAffy(filenames = samples.files, sampleNames = samples.animals, > > So I tested: > > length(samples.files); > [1] 4 > > length(samples.names); > [1] 4 > > Have I misunderstood the purpose of the sampleNames argument? Or > ss there > another way of changing the "column" names in an eSet and in > write.exprs() > output? > > Any suggestions much appreciated! > Paul > > ---------------------------------------- > This mail sent through www.mywaterloo.ca