Hi BioC User,

I am working for the first time on agilent CGH arrays (singel-channel).

I would like to use the limma package for that>

This is my script:
  >library(limma)

  >targets <- readTargets("targets.txt")
  >x <- read.maimages(targets, path="rawData/",
source="agilent",green.only=TRUE, names = targets$condition)
  >RG <- read.maimages(targets, path="rawData/", columns = list(G =
"gMedianSignal", Gb = "gBGMedianSignal", R = "gProcessedSignal",
   Rb = "gIsPosAndSignif"), annotation = c("Row", "Col","FeatureNum",
"ControlType","ProbeName"), names = targets$condition)

I tried both examples as I've found an explanation mentioning both of them (
here<http://matticklab.com/index.php?title=Single_channel_analysis_of_Agilent_microarray_data_with_Limma>).
My problem is that the results differs slightly from one another:

> RG
An object of class "RGList"
$G
     controll 5_4_chr5 5_3_chr5 5_4_cp 5_3_growth 5_3_cp 5_3_growth
[1,]    363.0    374.0     1647  678.0      498.5  505.0        642
[2,]     34.0     24.0       27   34.5       31.0   34.0         31
[3,]     29.5     23.0       23   30.0       26.0   26.5         30
[4,]     31.0     23.0       28   28.0       27.0   31.0         29
[5,]     31.0     25.5       28   27.0       32.0   29.0         31
45209 more rows ...

> x
An object of class "EListRaw"
$E
      controll  5_4_chr5   5_3_chr5    5_4_cp 5_3_growth    5_3_cp
5_3_growth
[1,] 361.30160 364.68250 1667.98200 683.31250  506.46670 502.66670
649.01610
[2,]  34.84483  25.94737   29.00000  35.54839   32.28571  33.16949
30.70492
[3,]  31.23438  25.46032   23.61905  31.90164   27.84127  28.95161
30.82540
[4,]  31.65000  24.31818   27.72414  31.83607   28.85484  31.39683
30.25000
[5,]  32.06349  25.93548   28.98413  28.25000   31.44615  28.04615
30.78462
45209 more rows ...

Even though the differences are very small, I would still like to
understand them.
If I understood the manual correctly, limma takes by default the median
column for both fore- and background.
The background values are similar (x$Eb and RG$Eb).

What columns does limma uses for the analysis?


I would appreciate the help

thanks
Assa

> sessionInfo()
R version 2.14.1 (2011-12-22)
Platform: x86_64-unknown-linux-gnu (64-bit)

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
 [7] LC_PAPER=C                 LC_NAME=C
 [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

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

other attached packages:
[1] limma_3.10.3        BiocInstaller_1.2.1

loaded via a namespace (and not attached):
[1] tools_2.14.1

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