Hi: I am trying to use affy package to normalize 79 hgu133a chips. I have R1.8.1 and affy 1.3 on windows 2000. I am trying to use justRMA( ) and keep getting error messages like this: "Cel file xxxxxx.cel does not seem to be of HG-U133A type". I stored 79 cel files in a vector called all.cel.files. Here is what I am getting: ================================================================ > library(affy) > data <- justRMA(filenames=all.cel.files) Error in read.probematrix(filenames = filenames) : Cel file XH2003031149A.cel does not seem to be of HG-U133A type ## This is the #46th chip in all my cel files. > data <-justRMA(filenames=all.cel.files[1:45]) Background correcting Normalizing Calculating Expression ## Works fine. > data1 <- justRMA(filenames=all.cel.files[46:50]) Error in read.probematrix(filenames = filenames) : Cel file XH2003030551A.cel does not seem to be of hg-u133a type # This is the # 47th chip. > data1 <- justRMA(filenames=all.cel.files[47:50]) Background correcting Normalizing Calculating Expression # Works again. ================================================================ If I put the problem chip in the position #1 it will be fine, but there're always other chips ran into the same problem. It's very strange to me. Even I could do several times justRMA( ) and merge them together later, I imagine it would not make sense in terms of normalization. Help, please! Xia

Yes it was the problem in the line of DatHeader=......HG-U133A.1sq the 46th cel file had it in lower case: hg-u133a.1sq, but others are in upper case. I corrected it and everything works fine now. Thanks for the help, Ben. Xia Ben Bolstad wrote: > Could you look in the header of your cel files? > > In particular look for the line that says > > DatHeader= > > look for something ending in .1sq > > Do they match between the 46th file and any of the other files. Matching > means exactly the same including capitialization. > > On Thu, 2004-05-06 at 13:07, Xia Han wrote: > > Hi: > > > > I am trying to use affy package to normalize 79 hgu133a chips. I > > have R1.8.1 and affy 1.3 on windows 2000. > > I am trying to use justRMA( ) and keep getting error messages > > like this: > > "Cel file xxxxxx.cel does not seem to be of HG-U133A type". > > > > I stored 79 cel files in a vector called all.cel.files. Here is > > what I am getting: > > ================================================================ > > > library(affy) > > > data <- justRMA(filenames=all.cel.files) > > Error in read.probematrix(filenames = filenames) : > > Cel file XH2003031149A.cel does not seem to be of > > HG-U133A type > > ## This is the #46th chip in all my cel files. > > > data <-justRMA(filenames=all.cel.files[1:45]) > > Background correcting > > Normalizing > > Calculating Expression > > ## Works fine. > > > data1 <- justRMA(filenames=all.cel.files[46:50]) > > Error in read.probematrix(filenames = filenames) : > > Cel file XH2003030551A.cel does not seem to be of > > hg-u133a type > > # This is the # 47th chip. > > > data1 <- justRMA(filenames=all.cel.files[47:50]) > > Background correcting > > Normalizing > > Calculating Expression > > # Works again. > > ================================================================ > > > > If I put the problem chip in the position #1 it will be fine, but > > there're always other chips ran into the same problem. It's very > > strange to me. Even I could do several times justRMA( ) and merge > > them together later, I imagine it would not make sense in terms > > of normalization. > > > > Help, please! > > > > Xia > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor@stat.math.ethz.ch > > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor