[BioC] Help with library(affy)

[James W. MacDonald]

Tillinghast, Guy, M.D. wrote:
> Is this an appropriate place to email my questions regarding affy?

Yes, but a more accurate subject line would be 'help with ReadAffy()'.

> 
> I have used the function "file" to retrieve a CEL file from by Windows platform C drive.  
> 
> x<-file(description="C:\ etc")

That doesn't retrieve a file - it opens a connection to a file, which is 
quite a different thing.

> 
> However, when using ReadAffy, my generated file appears to read as a symbol.
> 
> data<-ReadAffy(x)

Exactly, because that is what you are passing. According to the help 
page for ReadAffy(), you want to pass a character vector:

Arguments:

      ...: file names separated by comma.

filenames: file names in a character vector.

In addition, if your files aren't in the working directory, you can use 
the celfile.path argument. Again, from the help page:

celfile.path: a character denoting the path 'ReadAffy' should look for
           cel files

So you can pass a character vector that includes the path, or just point 
ReadAffy() to a directory that contains your celfiles and it will load 
them all in.

Best,

Jim



> 
> Error message: VECTOR_ELT() can only be applied to a 'list' not a 'symbol'
> 
> Also, I cannot find documentation on VECTOR_ELT().  I have looked in read.affybatch in R documentation.
> 
> Do I need an argument which will convince ReadAffy that x is indeed a list and not a symbol?
> Would a widget help?
> 
> Many thanks,
> Guy Tillinghast, MD
> 
> 
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-- 
James W. MacDonald, M.S.
Biostatistician
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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