Try either myData <- ReadAffy() or myData <- read.affybatch(files=list.celfiles()) Thanks, Ben On Wed, 2004-06-30 at 21:16, S Peri wrote: > hi Ben, > > All my CEL files are with .CEL extension. They are not > text files. When I open them they are exactly in the > same format as CEL (starting with [CEL] header). > > In addition to all the CEL files in the directory I > have all my CEL files, I had two other files with > names Cel_key.xls and breastCancerData_2.xls which I > changed them to Cel_key.txt and > breastCancerData_2.txt(both as tab delimited txt > files). > > Pls. suggest what I am doing wrong. > > Thanks > SP > > --- Ben Bolstad <bolstad@stat.berkeley.edu> wrote: > > how come your cel files end in .txt? are you sure > > they are cel files > > and not something else? What do you see if you open > > up one of the files. > > > > Also, for most people ReadAffy() is a better way > > then calling > > read.affybatch() since it will create the phenodata > > automatically. > > > > Ben > > > > > > > > > > > > On Wed, 2004-06-30 at 20:38, S Peri wrote: > > > Hello group, > > > I am trying to read my cel files using > > read.affybatch > > > method. > > > > > > I stored all my cel files, probe information file > > and > > > experiment file in one directory. > > > > > > I used the following commands: > > > > > > >fls = list.files() > > > >ab = read.affybatch(filenames=fls) > > > Error in initialize(value, ...) : Is > > > breastCancerData_2.txt really a CEL file? tried > > > reading as text, gzipped text and binary > > > In addition: Warning message: > > > Incompatible phenoData object. Created a new one. > > > in: read.affybatch(filenames = fls) > > > > > > > > > I am getting the above error. What could be > > > happening. > > > I am trying to analyze Mike West and Nievens > > Breast > > > cancer affy data (Duke University). > > > > > > Could any one please help me what is wrong here > > and > > > also how does a phenoData file look like. What is > > > phenoData. > > > > > > Please help. > > > > > > thank you > > > > > > SP > > > > > > _______________________________________________ > > > Bioconductor mailing list > > > Bioconductor@stat.math.ethz.ch > > > > > > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor > > -- > > Ben Bolstad <bolstad@stat.berkeley.edu> > > http://www.stat.berkeley.edu/~bolstad > > > > > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor -- Ben Bolstad <bolstad@stat.berkeley.edu> http://www.stat.berkeley.edu/~bolstad

Hello group, I am trying to normalize using expresso module and I am getting the following error. In fact I followed the example given at the bottom of help file. The following is what I get: > abcel.data.norm = expresso(abcel.data, bgcorrect.method = "rma", normalize.method = "constant", pmcorrect.method = "pmonly", summary.method = "avgdiff") background correction: rma normalization: constant PM/MM correction : pmonly expression values: avgdiff background correcting...Error in bg.correct(afbatch, method = bgcorrect.method) : No direct or inherited method for function "bg.correct" for this call Any suggestions where it is going wrong. Thank you. SP

Yes all your CEL files may end with .CEL extension. But look at the first line of your code : > > > >fls = list.files() So fls will contain the filenames of all files including .txt and other extensions (as you have already mentioned that you stored everything in one folder). So try using list.celfiles() or simply ReadAffy() or try this : list.files(pattern=".CEL") PS: Please use the assignment operator "<-" instead of "=" . On Thu, 2004-07-01 at 05:16, S Peri wrote: > hi Ben, > > All my CEL files are with .CEL extension. They are not > text files. When I open them they are exactly in the > same format as CEL (starting with [CEL] header). > > In addition to all the CEL files in the directory I > have all my CEL files, I had two other files with > names Cel_key.xls and breastCancerData_2.xls which I > changed them to Cel_key.txt and > breastCancerData_2.txt(both as tab delimited txt > files). > > Pls. suggest what I am doing wrong. > > Thanks > SP > > --- Ben Bolstad <bolstad@stat.berkeley.edu> wrote: > > how come your cel files end in .txt? are you sure > > they are cel files > > and not something else? What do you see if you open > > up one of the files. > > > > Also, for most people ReadAffy() is a better way > > then calling > > read.affybatch() since it will create the phenodata > > automatically. > > > > Ben > > > > > > > > > > > > On Wed, 2004-06-30 at 20:38, S Peri wrote: > > > Hello group, > > > I am trying to read my cel files using > > read.affybatch > > > method. > > > > > > I stored all my cel files, probe information file > > and > > > experiment file in one directory. > > > > > > I used the following commands: > > > > > > >fls = list.files() > > > >ab = read.affybatch(filenames=fls) > > > Error in initialize(value, ...) : Is > > > breastCancerData_2.txt really a CEL file? tried > > > reading as text, gzipped text and binary > > > In addition: Warning message: > > > Incompatible phenoData object. Created a new one. > > > in: read.affybatch(filenames = fls) > > > > > > > > > I am getting the above error. What could be > > > happening. > > > I am trying to analyze Mike West and Nievens > > Breast > > > cancer affy data (Duke University). > > > > > > Could any one please help me what is wrong here > > and > > > also how does a phenoData file look like. What is > > > phenoData. > > > > > > Please help. > > > > > > thank you > > > > > > SP > > > > > > _______________________________________________ > > > Bioconductor mailing list > > > Bioconductor@stat.math.ethz.ch > > > > > > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor > > -- > > Ben Bolstad <bolstad@stat.berkeley.edu> > > http://www.stat.berkeley.edu/~bolstad > > > > > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor >