[BioC] bug in overview function of made4

[Jenny Drnevich]

Hi,

I found a bug in the overview function from the made4 package. When I call 
overview with a marrayRaw object, I get the following error:

 > overview(RG.mRaw)
Error in switch(class(arraydata), matrix = { :
         object "intensities" not found

I traced this to the getdata function:

  }, marrayRaw = {
         if (require(affy, quiet = TRUE)) {
             nrslides = as.integer(ncol(arraydata at maRf))
             nrspots = as.integer(nrow(arraydata at maRf))
             tmp = matrix(NA, nrow = nrspots, ncol = 2 * nrslides)
             tmp[, (1:nrslides) * 2 - 1] = arraydata at maGf - 
intensities at maGb  #perhaps intensities should be arraydata?
             tmp[, (1:nrslides) * 2] = arraydata at maRf - 
intensities at maRb       #perhaps intensities should be arraydata?
         }
         as.data.frame(tmp)

     }

When I replace 'intensities' with 'arraydata' in these two lines, it works 
just fine.  Also, here's a suggested improvement - at least for 'marrayRaw' 
objects,
sample names don't currently get used. I added the following to the getdata 
function to so the samples will be labeled:

  }, marrayRaw = {
         if (require(affy, quiet = TRUE)) {
             nrslides = as.integer(ncol(arraydata at maRf))
             nrspots = as.integer(nrow(arraydata at maRf))
             tmp = matrix(NA, nrow = nrspots, ncol = 2 * nrslides)
             tmp[, (1:nrslides) * 2 - 1] = arraydata at maGf - arraydata at maGb
             tmp[, (1:nrslides) * 2] = arraydata at maRf - arraydata at maRb
             tmp.names = vector(mode = "character", length = 2 * nrslides)
             tmp.names[(1:nrslides) * 2 - 1] = 
paste("G",colnames(arraydata at maGf),sep="_")
             tmp.names[(1:nrslides) * 2] = 
paste("R",colnames(arraydata at maRf),sep="_")
             colnames(tmp) = tmp.names
         }
         as.data.frame(tmp)

     }

I'm enjoying the package, especially the html3D!

Cheers,
Jenny

 > sessionInfo()
R version 2.2.0, 2005-10-06, i386-pc-mingw32

attached base packages:
[1] "tools"     "methods"   "stats"     "graphics"  "grDevices" "utils"
[7] "datasets"  "base"

other attached packages:
          affy       convert        marray       Biobase         made4
       "1.8.1"       "1.4.0"       "1.8.0"       "1.8.0"       "1.4.0"
scatterplot3d          ade4         limma
      "0.3-24"       "1.4-0"       "2.4.4"
 >



Jenny Drnevich, Ph.D.

Functional Genomics Bioinformatics Specialist
W.M. Keck Center for Comparative and Functional Genomics
Roy J. Carver Biotechnology Center
University of Illinois

330 ERML
1201 W. Gregory Dr.
Urbana, IL 61801

Ph: 217-244-7355
FAX: 217-265-5066
Email: drnevich at uiuc.edu