[BioC] ReadAffy() function

[James W. MacDonald]

Hi Ron,

Ron Ophir wrote:
> Dear list users,
> 
>  
> 
> I am running ReadAffy() function under 
> 
>  
> 
> R version 2.10.0 (2009-10-26) 
> 
> i386-pc-mingw32 
> 
>  
> 
> locale:
> 
> [1] LC_COLLATE=Hebrew_Israel.1255  LC_CTYPE=Hebrew_Israel.1255   
> 
> [3] LC_MONETARY=Hebrew_Israel.1255 LC_NUMERIC=C                  
> 
> [5] LC_TIME=Hebrew_Israel.1255    
> 
>  
> 
> attached base packages:
> 
> [1] stats     graphics  grDevices utils     datasets  methods  
> 
> [7] base     
> 
>  
> 
> other attached packages:
> 
> [1] RColorBrewer_1.0-2 Heatplus_1.16.0    limma_3.2.1       
> 
> [4] affy_1.24.2        Biobase_2.6.1     
> 
>  
> 
> loaded via a namespace (and not attached):
> 
> [1] affyio_1.14.0        preprocessCore_1.8.0 tools_2.10.0        
> 
> 
>  
> 
>>From some reason the following code works
> 
>  
> 
> C.anno = read.delim(file="gal/Citrus.gal",stringsAsFactors=FALSE)
> 
> targets = read.delim(file="targets/Targets.txt",stringsAsFactors=FALSE)
> 
>  
> 
> C.raw =  ReadAffy(filenames = targets$FileName,
> 
>                   celfile.path = "data",
> 
>                   sampleNames =
> paste(targets$Target,targets$Repeat,sep="")
> 
>   )
> 
>  
> 
> C.raw at phenoData = new("AnnotatedDataFrame",data = targets)
> 
> C.raw at featureData = new("AnnotatedDataFrame",data = C.anno)
> 
>  
> 
> whereas this one
> 
>  
> 
> C.raw =  ReadAffy(filenames = targets$FileName,
> 
>                   celfile.path = "data",
> 
>                   sampleNames =
> paste(targets$Target,targets$Repeat,sep=""),
> 
>                   phenoData = new("AnnotatedDataFrame",data = targets),
> 
>                   featureData = new("AnnotatedDataFrame",data =C.anno)
> 
>   )
> 
>  
> 
>  
> 
> does not.
> 
>  
> 
> I get the following error message:
> 
>  
> 
> Error: the following are not valid files:
> 
>     data/new("AnnotatedDataFrame", data = C.anno)
> 
> In addition: Warning message:
> 
> In AllButCelsForReadAffy(..., filenames = filenames, widget = widget,  :
> 
>   sampleNames not same length as filenames. Using filenames as
> sampleNames instead
> 
>  
> 
>  
> 
> !! Targets and C.anno are data.frames, since they were read by
> read.delim() function.
> 
>  
> 
> Can you think of why is that?

Sure. You are passing a non-existent argument to a function that has the 
ellipsis (...) as its first argument. In this case, the ellipsis is 
there to allow ReadAffy() to accept comma-delimited file names.

What is happening is that featureData = new("AnnotatedDataFrame", data = 
C.anno) is being parsed and (attempted to be) added to the vector of 
file names. Since the parsed value isn't a valid file you get the first 
error. Since your sampleNames and filenames are now different, you get 
the second warning.

Take home lesson: don't add fictitious arguments to ReadAffy().

Best,

Jim


> 
>  
> 
>  
> 
> Thanks, 
> 
> Ron
> 
>  
> 
>  
> 
> 
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> 
> 
> 
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> 
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-- 
James W. MacDonald, M.S.
Biostatistician
Douglas Lab
University of Michigan
Department of Human Genetics
5912 Buhl
1241 E. Catherine St.
Ann Arbor MI 48109-5618
734-615-7826
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