Entering edit mode
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
[[alternative HTML version deleted]]
Hi Gordon, Thanks for the answer, but the question is over 5 years old. You have already answered this one then.
May I ask why now?
The Bioconductor support website separated the question from the answer when converting from the old email archive. I added a link so that someone landing on this question now or in the future would know that it was answered. I sometimes do this when I see separated question-answer pairs.