[BioC] Rat Gene 1.0 ST

[Benilton Carvalho]

(apologies in case my initial attempt of sending this message went  
through)

Dear German,

I apologize for the inconvenience this may have caused.

The problem you reported is restricted to the image method. I'll  
submit the fix tonight and it'll be up, let's say, in about 2 days for  
download.

In the meantime, if you want a temporary fix, please copy/paste the  
following code after loading oligo:

setMethod("image", signature(x="FeatureSet"),
                  function(x, which=0, transfo=log2, col=gray((0:64)/ 
64), ...){
              if (which == 0){
                  which <- 1:length(x)
              }
              if(length(which) > 1) par(ask=TRUE) else par(ask=FALSE)
              theDim <- geometry(getPD(x))
              for (i in which){
                tmp <- matrix(transfo(exprs(x[,i])), ncol=theDim[1],  
nrow=theDim[2])
                tmp <- as.matrix(rev(as.data.frame(tmp)))
                image(tmp, col=col, main=sampleNames(x)[i], xaxt="n",  
yaxt="n", ...)
              }
              par(ask=FALSE)
            })


Thank you very much for your report,

b


On Aug 14, 2009, at 5:41 PM, Germán González wrote:

> Hi everybody!
>
> I'm a beginner in the analysis and interpretation of microarray  
> data. I've been working with a Affymetrix's GeneChip® Rat Gene 1.0  
> ST Array and I have a doubt
> about the image that you get when using the command "image". There's  
> two holes in the middle of the image, is this normal?
>
> Regards
> Germán
>
> <microarray.png><ATT00001.txt>