[BioC] (microarray) - affylmGUI error when reading Affymetrix U133A and U133B .CEL file

[James W. MacDonald]

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) http://bioinf.wehi.edu.au/affylmGUI/R/library/affylmGUI/doc/estrogen/estrogen.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
>
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-- 
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
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Seattle WA 98105-6099