Entering edit mode
Guido Hooiveld
★
4.1k
@guido-hooiveld-2020
Last seen 1 day ago
Wageningen University, Wageningen, the …
Hi,
I would like to use limma's neqc function for background correction of
a set of single colour Agilent arrays obtained from GEO (GSE27784).
However, I am not able to get it to work, likely due to a simple issue
which I am not able to tackle. Therefore, any pointers to get it
running would be appreciated.
Regards,
Guido
> library("limma")
>
> targets <- readTargets("targets_GSE27784.txt", row.names="Name")
> e.raw <- read.maimages(targets$FileName, source="agilent.median",
green.only=TRUE)
Read GSM686624_251486829200_S01_GE1_105_Jan09_1_1.txt
Read GSM686625_251486829201_S01_GE1_105_Jan09_1_2.txt
Read GSM686626_251486829328_S01_GE1_105_Jan09_1_3.txt
Read GSM686627_251486829200_S01_GE1_105_Jan09_1_2.txt
Read GSM686628_251486829200_S01_GE1_105_Jan09_1_4.txt
Read GSM686629_251486829201_S01_GE1_105_Jan09_1_4.txt
Read GSM686630_251486829328_S01_GE1_105_Jan09_1_4.txt
Read GSM686631_251486829328_S01_GE1_105_Jan09_1_1.txt
Read GSM686632_251486829328_S01_GE1_105_Jan09_1_2.txt
Read GSM686633_251486829200_S01_GE1_105_Jan09_1_3.txt
Read GSM686634_251486829201_S01_GE1_105_Jan09_1_3.txt
Read GSM686635_251486829201_S01_GE1_105_Jan09_1_1.txt
>
> # Specify neg cons because they are different than what limma
expects
> bg.corr <- neqc(e.raw, status=e.raw$genes$SystematicName,
negctrl="NegativeControl")
Error in if (alpha <= 0) stop("alpha must be positive") :
missing value where TRUE/FALSE needed
>
> # confirm Negative Controls are indeed present in input file
> e.raw$genes$SystematicName[550:560]
[1] "NM_001029937" "NM_029372" "NM_178076"
"NegativeControl" "NM_032418" "XM_991644"
[7] "AK036031" "AF012177" "NM_178257"
"NM_001038845" "NM_019764"
>
> e.raw
An object of class "EListRaw"
$E
GSM686624_251486829200_S01_GE1_105_Jan09_1_1
GSM686625_251486829201_S01_GE1_105_Jan09_1_2
GSM686626_251486829328_S01_GE1_105_Jan09_1_3
GSM686627_251486829200_S01_GE1_105_Jan09_1_2
[1,] 18713.5
14800 20646.4
19689
[2,] 27.0
24 25.0
26
[3,] 24.5
23 22.0
25
[4,] 26.0
24 23.0
24
[5,] 26.0
23 23.0
24
<<snip>>
45013 more rows ...
$Eb
GSM686624_251486829200_S01_GE1_105_Jan09_1_1
GSM686625_251486829201_S01_GE1_105_Jan09_1_2
GSM686626_251486829328_S01_GE1_105_Jan09_1_3
GSM686627_251486829200_S01_GE1_105_Jan09_1_2
[1,] 19
16 17.5
20
[2,] 20
17 18.0
20
[3,] 21
17 19.0
20
[4,] 21
17 18.0
21
[5,] 20
17 17.0
21
<<snip>>
45013 more rows ...
$targets
[1] "GSM686624_251486829200_S01_GE1_105_Jan09_1_1.txt"
"GSM686625_251486829201_S01_GE1_105_Jan09_1_2.txt"
"GSM686626_251486829328_S01_GE1_105_Jan09_1_3.txt"
"GSM686627_251486829200_S01_GE1_105_Jan09_1_2.txt"
[5] "GSM686628_251486829200_S01_GE1_105_Jan09_1_4.txt"
7 more rows ...
$genes
Row Col ControlType ProbeName SystematicName
1 1 1 1 GE_BrightCorner GE_BrightCorner
2 1 2 1 DarkCorner DarkCorner
3 1 3 1 DarkCorner DarkCorner
4 1 4 1 DarkCorner DarkCorner
5 1 5 1 DarkCorner DarkCorner
45013 more rows ...
$source
[1] "agilent.median"
>
> sessionInfo()
R version 2.14.0 (2011-10-31)
Platform: i386-pc-mingw32/i386 (32-bit)
locale:
[1] LC_COLLATE=English_United States.1252
[2] LC_CTYPE=English_United States.1252
[3] LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C
[5] LC_TIME=English_United States.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] limma_3.10.0
>
---------------------------------------------------------
Guido Hooiveld, PhD
Nutrition, Metabolism & Genomics Group
Division of Human Nutrition
Wageningen University
Biotechnion, Bomenweg 2
NL-6703 HD Wageningen
the Netherlands
tel: (+)31 317 485788
fax: (+)31 317 483342
email: guido.hooiveld@wur.nl
internet: http://nutrigene.4t.com
http://scholar.google.com/citations?user=qFHaMnoAAAAJ
http://www.researcherid.com/rid/F-4912-2010
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