[BioC] Read Agilent 244k chip and QC

[Juan Carlos Oliveros]

Dear Marc,

There is a previous answer to another user with the same problem.

Source:
https://stat.ethz.ch/pipermail/bioconductor/2007-January/015532.html

I paste the text here (original by Dr. Gordon K Smyth)

---8<--------------

The error message is telling you that there aren't enough rows of data for the size of the block. 
The reason is that Agilent doesn't print rows for blank spots and the like, so the block has
missing rows, and this causes a problem because the limma functions assume complete blocks.

BTW, this is why the function read.maimages() didn't set the $printer information automatically
for you.  If the file had contained complete data for the block, then it would have.

It is possible with a little R programming to expand out your data vector stuff$Rb[,1] to be the
right length by adding NAs in the right places, so that you could use imageplot(), but this bit of
code is not provided by limma or Bioconductor.  Try this:

  r <- stuff$genes$Row
  c <- stuff$genes$Col
  nr <- max(r)
  nc <- max(c)
  y <- rep(NA,nr*nc)
  i <- (r-1)*nc+c
  y[i] <- log2(stuff$Rb[,1])
  imageplot(y,stuff$printer)

Best wishes
Gordon



--->8--------------

I hope that helps,

Best,

Juan Carlos Oliveros, Ph.D
CNB-CSIC, Madrid, Spain



Marc Noguera wrote:
> Hi all,
> I am trying to read and visualize data obtained from an agilent chip.
>
> For this purpose I use limma package and the read.maimages function as
> follows
>
> fileRG.raw <- read.maimages("File",source="agilent")
>
> FileRG gets read correctly. When I check the dimensions it shows to have
> 243494 probes which seem to be correctly annotated. I, then attach the
> layout for the chip from the GAL file:
>
> galinfo <- readGAL(fileGAL)
> fileRG.raw$printer<-getLayout(galinfo)
>
> and try to plot R/G according to this prnter layout:
>
> imageplot(log2(fileRG.raw$R),fileRG.raw$printer,zlim=c(0,9),main="R-For.RAW")
>
> However, I obtain the following error:
>
>   
>> Error in imageplot(log2(fileRG.raw$R), fileRG.raw$printer, zlim = c(0,  :
>>   Number of image spots does not agree with layout dimensions
>>     
> Which is due to the fact that the gal file has 912*267 dimension
> corresponding to 243504 probes. Checking the expression raw information
> I see that there are 10 probes that are tagged as "ignore", which
> read.maimages ignores convenientl but, then, I can't visualize R and G
> channels (or MA info when obtained) because of this inconsistency.
> If I add, by hand, ten probes in the expression file, imageplot works
> fine but this is not the right thing to do.
>
> What is the convenient thing to do? Any suggestion?
>
> Thank you in advance
>
> Marc
>
>