(microarray) - affylmGUI error when reading Affymetrix U133A and U133B .CEL file
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Zack Will ▴ 30
@zack-will-5491
Last seen 6.8 years ago
United Kingdom
Hi Everybody, I am using the affylmGUI to read .CEL files. However I encountered an error (shown below) if Affymetrix U133A and Affymetrix U133B .CEL file are both present in one "target tab-delimited text format"*. The error is. "Error in read.affybatch(filenames = ;$filenames, phenoData = l$phenoData, : Cel file <cel file="" name="">l does not seem to be of HG- U133A type" or "Error in read.affybatch(filenames = ;$filenames, phenoData = l$phenoData, : Cel file <cel file="" name="">l does not seem to be of HG- U133B type" *target tab-delimited text format - is a text format file required for affylmGUI (as described from a worked example dataset tutorial) http:/ /bioinf.wehi.edu.au/affylmGUI/R/library/affylmGUI/doc/estrogen/estroge n.html However if in the "target tab-delimited text format" only contains the U133A type or only contains the U133B type, the affylmGUI would work fine. It may also worth mentioning that my background in R is very minimal (only one week) and the affylGUI interface is helping in the learning curve process to look at microarray data. Any help or suggestion from the members would be greatly appreciative! Many Thanks Zaki
Microarray PROcess affylmGUI Microarray PROcess affylmGUI • 790 views
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@james-w-macdonald-5106
Last seen 2 hours ago
United States
Hi Zaki, On 9/10/2012 9:09 PM, Zaki Fadlullah wrote: > Hi Everybody, > > I am using the affylmGUI to read .CEL files. However I encountered an error (shown below) if Affymetrix U133A and Affymetrix U133B .CEL file are both present in one "target tab-delimited text format"*. The error is. > > "Error in read.affybatch(filenames = ;$filenames, phenoData = l$phenoData, : Cel file<cel file="" name="">l does not seem to be of HG- U133A type" > > or > > "Error in read.affybatch(filenames = ;$filenames, phenoData = l$phenoData, : Cel file<cel file="" name="">l does not seem to be of HG- U133B type" > > > *target tab-delimited text format - is a text format file required for affylmGUI (as described from a worked example dataset tutorial) ht tp://bioinf.wehi.edu.au/affylmGUI/R/library/affylmGUI/doc/estrogen/est rogen.html > > > However if in the "target tab-delimited text format" only contains the U133A type or only contains the U133B type, the affylmGUI would work fine. > > It may also worth mentioning that my background in R is very minimal (only one week) and the affylGUI interface is helping in the learning curve process to look at microarray data. Any help or suggestion from the members would be greatly appreciative! As you have noted, you cannot process two different chip types simultaneously. The easiest thing to do is just analyze each chip set separately, and if you want you can combine data at the end. Best, Jim > > > Many Thanks > Zaki > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- James W. MacDonald, M.S. Biostatistician University of Washington Environmental and Occupational Health Sciences 4225 Roosevelt Way NE, # 100 Seattle WA 98105-6099
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