Hello,

I'm having trouble analyzing my custom arrays with limma.  I've searched
the archives and I seem to be running into a similar problem that was
previously dealt with here (
https://stat.ethz.ch/pipermail/bioconductor/2005-October/010482.html).

I'm also using outputs from a scanarray express, although I've modified my
.csv's accordingly and removed the final line of useless data as indicated
in the archives.  Also, being an R newbie I wasn't sure how to tell R that
my data started after some 74 lines of headers (output info from the
scanner), so I deleted those headers out as well (and input $printer info
manually), leaving only a header for the columns of intensity data.   For
simplicities sake I've pasted below a shortened session of what I'm trying
to do (my apologies for the lengthy e-mail).  I appreciate the help and
comments.



R version 2.14.0 (2011-10-31)
Copyright (C) 2011 The R Foundation for Statistical Computing
ISBN 3-900051-07-0
Platform: i386-apple-darwin9.8.0/i386 (32-bit)
[R.app GUI 1.42 (5933) i386-apple-darwin9.8.0]

> setwd("***")
> library(limma)
> targets<-readTargets()
> RG <-read.maimages(targets, source="scanarrayexpress",annotation=c("Array
Row", "Array Column", "Spot Row", "Spot Column", "Name", "ID"),
other.columns=c("Ch1 SignalNoiseRatio", "Ch2 SignalNoiseRatio"), sep=",")
Read 01-13_B.csv
Read 01-13_M.csv
Read 01-13_T.csv
> RG$printer <-getLayout2("ChinookBOT.gal")
> spottypes<-readSpotTypes()
> RG$genes$Status<- controlStatus(spottypes, RG)
Matching patterns for: Name
Found 1116 oligo
Found 21 blank
Found 15 serial
Setting attributes: values Color
> show(RG)
An object of class "RGList"
$G
     01-13_B 01-13_M 01-13_T
[1,]     102     119     239
[2,]     100     122     339
[3,]     102     135     251
[4,]      90     112     242
[5,]     110     141     239
1147 more rows ...

$Gb
     01-13_B 01-13_M 01-13_T
[1,]      89      94     147
[2,]      88      84     181
[3,]      88      91     161
[4,]      92      90     175
[5,]      86      87     154
1147 more rows ...

$R
     01-13_B 01-13_M 01-13_T
[1,]     120     678     202
[2,]     154     610     312
[3,]     146     614     306
[4,]     108     654     310
[5,]     122     710     291
1147 more rows ...

$Rb
     01-13_B 01-13_M 01-13_T
[1,]     108     119     135
[2,]     109     137     159
[3,]     113     124     169
[4,]     115     124     180
[5,]     119     104     159
1147 more rows ...

$targets
     FileName Cy3 Cy5
1 01-13_B.csv  B1  B2
2 01-13_M.csv  M1  M2
3 01-13_T.csv  T1  T2

$genes
  Array Row Array Column Spot Row Spot Column     Name      ID Status
1         1            1        1           1 HEATH049 Gene A4  oligo
2         1            1        1           2 HEATH049 Gene A4  oligo
3         1            1        1           3 HEATH049 Gene A4  oligo
4         1            1        1           4 HEATH113 Gene A8  oligo
5         1            1        1           5 HEATH113 Gene A8  oligo
1147 more rows ...

$source
[1] "scanarrayexpress"

$other
$Ch1 SignalNoiseRatio
     01-13_B 01-13_M 01-13_T
[1,]    3.06    2.55    3.02
[2,]    2.72    3.06    2.35
[3,]    2.68    3.60    3.34
[4,]    2.51    3.12    0.95
[5,]    3.33    3.82    2.66
1147 more rows ...

$Ch2 SignalNoiseRatio
     01-13_B 01-13_M 01-13_T
[1,]    2.31   12.41    2.85
[2,]    2.42   11.82    3.57
[3,]    2.66   11.71    4.14
[4,]    1.75   14.41    0.65
[5,]    2.09   15.90    4.62
1147 more rows ...


$printer
$ngrid.r
[1] 4

$ngrid.c
[1] 4

$nspot.r
[1] 6

$nspot.c
[1] 14


> MA<- normalizeWithinArrays(RG)
Error in normalizeWithinArrays(RG) :
  printer layout information does not match M row dimension



-- 
Matthew Ouellette, M.Sc. Candidate
Great Lakes Institute for Environmental Research
University of Windsor

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