Question about using ReadAffy() to read CEL files
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Xiaoyu Jia ▴ 20
@xiaoyu-jia-1149
Last seen 9.6 years ago
Dear friends, I am trying to read CELfiles using ReadAffy() command. I stored all my CEL files in a directory and use the following commands: >library(affy) >mydata<-ReadAffy() Error in read.affybatch(filenames = l$filenames, phenoData = l$phenoData, : Is C:/Documents and Settings/Desktop/kumar/data03-15/Kumar 001.CEL really a CEL file? tried reading as text, gzipped text and binary I do not understand why this happened. Could anybody help me out? Thank you very much. Sharrie ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues.
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@james-w-macdonald-5106
Last seen 28 minutes ago
United States
Xiaoyu Jia wrote: > Dear friends, > > I am trying to read CELfiles using ReadAffy() command. I stored all my > CEL files in a directory and use the following commands: > > >>library(affy) >>mydata<-ReadAffy() > > Error in read.affybatch(filenames = l$filenames, phenoData = > l$phenoData, : > Is C:/Documents and Settings/Desktop/kumar/data03-15/Kumar > 001.CEL really a CEL file? tried reading as text, gzipped text and > binary Odd. I don't have any problems reading in these files. > dat <- ReadAffy() > sampleNames(dat) [1] "Kumar 001.CEL" "Kumar 002.CEL" "Kumar 003.CEL" "Kumar 004.CEL" "Kumar 005.CEL" "Kumar 006.CEL" [7] "Kumar 007.CEL" "Kumar 008.CEL" It may be that they are corrupted. Are they all ~2786 Kb in size? Jim > > > I do not understand why this happened. Could anybody help me out? > > Thank you very much. > > Sharrie > > > ********************************************************** > Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues. > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor -- James W. MacDonald Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623
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> > > > Error in read.affybatch(filenames = l$filenames, phenoData = > > l$phenoData, : > > Is C:/Documents and Settings/Desktop/kumar/data03-15/Kumar > > 001.CEL really a CEL file? tried reading as text, gzipped text and > > binary > This message would be typical of corrupt files.
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Xiaoyu Jia ▴ 20
@xiaoyu-jia-1149
Last seen 9.6 years ago
Dear friends, I am trying to read CELfiles using ReadAffy() command. I stored all my CEL files in a directory and use the following commands: >library(affy) >mydata<-ReadAffy() Error in read.affybatch(filenames = l$filenames, phenoData = l$phenoData, : Is C:/Documents and Settings/Desktop/kumar/data03-15/Kumar 001.CEL really a CEL file? tried reading as text, gzipped text and binary I do not understand why this happened. Could anybody help me out? Thank you very much. Sharrie ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues.
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One thing you might try is excluding this file and trying to read the remaining celfiles in that directory (that way you can see if it is just that file that is problematic or all your files). one way to do that would be mydata <- ReadAffy(filenames=list.celfiles[-1]) On Wed, 2005-03-16 at 12:39 -0500, Xiaoyu Jia wrote: > Dear friends, > > I am trying to read CELfiles using ReadAffy() command. I stored all my > CEL files in a directory and use the following commands: > > >library(affy) > >mydata<-ReadAffy() > Error in read.affybatch(filenames = l$filenames, phenoData = > l$phenoData, : > Is C:/Documents and Settings/Desktop/kumar/data03-15/Kumar > 001.CEL really a CEL file? tried reading as text, gzipped text and > binary > > > I do not understand why this happened. Could anybody help me out? > > Thank you very much. > > Sharrie > > > ********************************************************** > Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues. > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor
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