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Stefanie Busch
▴
10
@stefanie-busch-6387
Last seen 10.3 years ago
Hello,
I'm Stefanie from Germany. So excuse me when my english isn't very
well.
I want to normalize the raw data of the GEO experiment "GSE39313".
In this
experiment the Illumina MouseRef-8 v2.0 expression beadchip was
used. I get
the data with getGEOSuppFiles but I don't know what I should do
next. I know
that I can analyse Illumina chips with the packages beadarray, lumi
or
limma. I have uploaded the raw.txt-file with the different
packages.
For example:
> Daten.lumi<-lumiR(file="GSE39313_non-normalized.txt")
Please provide Illumina ID Mapping library!
> Daten.lumi
ExpressionSet (storageMode: lockedEnvironment)
assayData: 25697 features, 48 samples
element names: detection, exprs
protocolData: none
phenoData
sampleNames: 7539447003_A 7539447003_B ... 7917911031_H (48
total)
varLabels: sampleID
varMetadata: labelDescription
featureData
featureNames: ILMN_2896528 ILMN_2721178 ... ILMN_2424408 (25697
total)
fvarLabels: ID_REF
fvarMetadata: labelDescription
experimentData: use 'experimentData(object)'
Annotation:
As you can see I have no Annotation information. GEO provide the
bgx.file
for the Chip (Illumina MouseRef-8 v2.0 expression beadchip) but I
don't know
how to connect this. I tried this:
>
Daten.lumi2<-addNuID2lumi(Daten.lumi,annotationFile="MouseRef-
8_V2_0_R3_1127
8551_A.bgx")
> Daten.lumi2
ExpressionSet (storageMode: lockedEnvironment)
assayData: 25697 features, 48 samples
element names: detection, exprs
protocolData: none
phenoData
sampleNames: 7539447003_A 7539447003_B ... 7917911031_H (48
total)
varLabels: sampleID
varMetadata: labelDescription
featureData
featureNames: WpaZ9x9f_hAnoR.VBE ZhdXp75JftSF3iWLF4 ...
Zl4J4B0PsjTJ1N19IM (25697 total)
fvarLabels: ID_REF
fvarMetadata: labelDescription
experimentData: use 'experimentData(object)'
Annotation:
But there are again no annotation Information. And when I used the
exprs()
function I get this what looks very strange:
> head(exprs(Daten.lumi2))
7539447003_A 7539447003_B 7539447003_C
7539447003_D
WpaZ9x9f_hAnoR.VBE 4476.8840 5870.2020 5149.9380
5193.5800
ZhdXp75JftSF3iWLF4 970.4051 1032.8760 1132.4740
1280.3510
xnx7ijE2CcOSlY55eA 1577.7980 1511.4770 1711.2830
1850.6020
xPkUXaq37oR_vSi6HY 9862.2040 11187.4000 12783.4400
14389.9900
3rtRBd9AcK1Qq07fGI 222.3842 236.7587 210.8107
229.3236
ZqRKnn0K14kTIep1.c 3877.7640 5116.4140 6129.5220
2486.4500
So I tried to use limma:
>
Daten.limma<-read.ilmn(files="GSE39313_non-
normalized.txt",other.columns="De
tection Pval")
This works well, but I don't know where to get the bgx.file in. And
the
further problem is, when I want to normalize according to the
instructions
of BeadArrayUseCases page 25 I get this error message:
> maqc.norm<-neqc(Daten.limma)
Fehler in normexp.fit.detection.p(x, detection.p) :
Detection p values not found in the data.
Please can you tell me where is my mistake?
Stefanie