[BioC] problems of hgu95a

[Adaikalavan Ramasamy]

I had this problem before and I can think of two reasons
a) the file was somehow corrupted (e.g. during download).
b) the files do truly come from two different cel types

It is easy to check b). Open up the cel files in notepad or a
spreadsheet. In the middle of line of line 18 or 19, you should see
something like "HG_U95Av2.1sq" which indicates that it is from HGU95av2.
Now repeat for a few CEL files. If it comes from two different types,
then you might want to double check with the authors.

There is no need to go back to R-1.9.0 because I think you are going to
face the same problems and risk not getting updated packages.

I believe that there is one extra probeset HGU95A and HGU95av2. I am
sure there must be other differences, otherwise Affy would not have
released a new version. Perhaps others on the list know.

Regards, Adai



On Tue, 2005-07-12 at 17:59 -0700, weinong han wrote:
> Dear All, 
> 
> I am analyzing Cromer A, Carles A et al. hypopharyngeal cancer data at various stages of progression. In their Oncogene paper (2004 Apr 1;23(14):2484-98), they mentioned  they used hgu95a chip.When I loaded the all .cel files into R 2.1.0(OS:windows XP), I was told that:
> library(affy) 
> Data <- ReadAffy() 
> Error in initialize(value, ...) : Cel file D:/GSE2379_CEL/GSM44799.CEL does not seem to be of HG_U95Av2 type.
> 
> Overall, 18 .cel files like GSM44799 do not seem to be of HG_U95Av2 type.
> 
> Why happened so? I should go back to low version R like R1.9.0? What difference between HG_U95A and HG_U95Av2 type?
> 
> How to fix it? 
> 
> please help me and thank you.
> 
>  
> 
> 
> 
> Best Regards
>  
> Han Weinong  
> hanweinong at yahoo.com
> 
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