[BioC] Limma, marray and Agilent 44K

[Nataliya Yeremenko]

Dear members of the Bioconductor mail-list
dear maintainers of the limma and marray packages

I wonder if there is proper handling of the Agilent 44K arrays is 
implemented in marray.
Meanwhile I'm analyzing my human 44K in limma,
and everything works fine with a great help of the list and almost 
perfect userguide
(I'm rather biologist, than bioinformatician).
Than the question appears to try "globalMAD" normalization from marray.
Excited with limma userguide words about easy conversion of the RGlist 
data to marrayRaw object.
I started in LIMMA like this:
 >RG.raw <- read.maimages(files = targets$fileName, path = loadPath, 
source = "agilent", quote="")
...
 >dim(RG.raw)
[1] 43931    29
 >RG.raw$genes$Status <- controlStatus(spottypes, RG.raw)
Matching patterns for: ControlType
Found 43931 Probe
Found 314 Negative
Found 1942 Positive
Setting attributes: values Color

SEEMS FINE so far

 > data.raw <- as(RG.raw, "marrayRaw")
 > summary(data.raw)
...
A) Layout of spots on the array:
Array layout:    Object of class marrayLayout.
Total number of spots:                 
Dimensions of grid matrix:               rows by  cols
Dimensions of spot matrices:             rows by  cols
Currently working with a subset of spots.
Control spots:
There are   3 types of controls :
Negative Positive    Probe
     314     1942    41675
Notes on layout:
...
 > data.norm <- maNorm(data.raw,norm="loess",echo=TRUE)
Normalization method: loess.
Normalizing array 1.
Error in if (is.int(totalPlate)) { : argument is of length zero

OOPS :) Petty, It seems that marrayLayout is wrong.

Than I thought that import of the data is implemented better than the 
conversion in marray I tried in frame of MARRAY:
 > data.marray.raw <- read.Agilent(fnames=targets$fileName, quote="")
 > summary(data.marray.raw)
...
A) Layout of spots on the array:
Array layout:    Object of class marrayLayout.
Total number of spots:                  12900
Dimensions of grid matrix:              1 rows by 1 cols
Dimensions of spot matrices:            30 rows by 430 cols
Currently working with a subset of 12797spots.
Control spots:
There are   3 types of controls :
Negative Positive   probes
      47      311     5837
Notes on layout:  

ONCE again, something wrong with layout

However maNorm() is working w/o reported mistakes,
but I wonder what is it normalising...

Does anybody have any  clue how to deal with Agilent 44K within marray?
I searched for the archive, and did find the rare discussions on this,
but didn't find the answer.

I wonder as well if this problem is fixed in the developing version of 
the MARRAY

And finaly, as advised below is
 > sessionInfo()
R version 2.2.1, 2005-12-20, i386-pc-mingw32

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

other attached packages:
 convert   marray      vsn  Biobase   gplots    gdata   gtools    limma
 "1.4.0"  "1.8.0"  "1.8.0"  "1.8.0"  "2.3.0"  "2.1.2"  "2.2.3" "2.4.13"
 >

Waiting for advices...

-- 

Dr. Nataliya Yeremenko 

Universiteit van Amsterdam
Faculty of Science
IBED/AMB (Aquatische Microbiologie)
Nieuwe Achtergracht 127
NL-1018WS Amsterdam
the Netherlands

tel. + 31 20 5257089
fax  + 31 20 5257064