  Dear All,

  I am trying to use the arrayQuality package with a set of two-color
Agilent arrays (G2519F AMADID 014868 MOUSE 4x44), but I am just getting an
error which I do not know how to overcome. Some details of the attempts we
made:

  R version: 2.10.1 (also tried on 2.7.0)
  Packages version: arrayQuality_1.24.0, limma_3.2.3, RColorBrewer_1.0-2,
gridBase_0.4-3, hexbin_1.22.0, lattice_0.18-3, convert_1.22.0,
Biobase_2.6.1, marray_1.24.0
  Raw data format: txt files obtained with the "Feature Extraction" Agilent
software (You can have a look at the file header here:
http://bioinformatics.fcrb.es/documentacion/header.txt).

  We first tried to use the agQuality function:

> agQuality("US85003608_251486821883_S01_GE2-v5_10_Apr08_1_1.txt")
[1] "Starting agQuality..."
Reading ...  ./US85003608_251486821883_S01_GE2-v5_10_Apr08_1_1.txt
Error in slideQuality(gp, controlMatrix = controlMatrix, DEBUG = DEBUG) :
  dims [product 45018] do not match the length of object [0]

  It seemed that there were some kind of problem with file format, so we
tried to do it by reading with read.maimages and then using maQualityPlots:

>
RG<-read.maimages("US85003608_251486821883_S01_GE2-v5_10_Apr08_1_1.txt","agilent",columns
= list(G = "gMedianSignal",Gb = "gBGMedianSignal",R
="rMedianSignal",Rb="rBGMedianSignal"),other.columns=c("gIsPosAndSignif","rIsPosAndSignif"),annotation=
c("Row","Col","ProbeUID","ProbeName","GeneName","accessions","SystematicName","ControlType"))
# This text file corresponds to one of the four arrays in the slide
Read US85003608_251486821883_S01_GE2-v5_10_Apr08_1_1.txt
> colnames(RG$genes)[2] <- "Column"
> RG$genes$Block <- rep(1, length(RG$genes$ProbeName)) # There is only one
block in the array
> RG$printer <- getLayout(RG$genes)
> maQualityPlots(RG)
Error: dims [product 45018] do not match the length of object [45220]
In addition: Warning messages:
1: In samplesub & which :
  longer object length is not a multiple of shorter object length
2: In samplesub & which & subset & good :
  longer object length is not a multiple of shorter object length

  It seems to be a problem with the array layout. There are only 45022
rows(probes) in the txt file from which 45018 are read by read.maimage, but
also, the maximum row and column coordinates of the spots are 532 and 85
respectively. Multiplying 532x85 gives 45220, which is the expected size of
the complete array. So, is it possible that the "Feature Extraction"
software is filtering out some spots? Is it possible to run maQualityPlots
if these spots are missing? Any clue?

  Thank you very much.

  Regards,

  F. Javier Lopez

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