[BioC] limma: read.imagene patch

Gordon Smyth smyth at wehi.edu.au
Thu Oct 2 19:23:25 MEST 2003

I have implemented this in limma 1.2.7.


At 10:43 PM 1/10/2003, Yves Bastide wrote:
>Gordon Smyth wrote:
>>Dear Yves,
>>Thanks for the suggested code changes. Before I make commit changes to 
>>the code, would you mind showing me an example of some headers which 
>>change length? I know that different versions of Imagene produce 
>>different headers, but read.imagene() like read.maimages() is designed to 
>>read a batch of arrays which should in principle have the same layout, so 
>>I would be uncomfortable about users reading in unrelated arrays. I just 
>>want to see in what ways the header can change within one experiment.
>You're right, this patch is way too broad; I don't think the headers for 
>the cy3 and cy5 files of a measure can change.
>>Note also that if you have two batches of arrays scanned with different 
>>settings, you can read them into two RGList objects and then combine the 
>>objects using cbind.
>This is the case I met, with slightly different quality settings between 
>the first and subsequent scans.  I think it'd be convenient having 
>read.imagene() handle this.
>for (i in 1:narrays) {
>   fullname <- ...
>+  headers <- getImageneHeaders(fullname)
>+  if (headers$Field.Dimensions[...] != printer) error(...)
>+  skip <- headers$Begin.Raw.Data
>   obj<-read.table(...)

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