Entering edit mode
Stephen Rolfe
▴
20
@stephen-rolfe-5431
Last seen 8.4 years ago
I have a set of files from the new Aragene-1_1-st microarrays. I am
using
oligo to analyse these but have hit a problem with the annotation.
I have the most up-to-date packages and don't hit any error messages.
However, using getNetAffx doesn't seem to add annotation data to my
rma
normalised data set.
The feature labels are all there and the probsetids have been set. All
of
the other data are NA.
Any insight would be much appreciated. Eventually I want to analyse
the data
in limma.
(I tried building my own pd files using pdinfoBuilder as an
alternative, but
hit a bunch of error messages that I couldn't overcome.)
Thanks for your help
Steve Rolfe
R version 2.15.1 (2012-06-22) -- "Roasted Marshmallows"
> library("pd.aragene.1.1.st")
> library(oligo)
> library(Biobase)
> celfiles<-list.celfiles()
> affyRaw<-read.celfiles(files=celfiles)
Platform design info loaded.
Reading in : WT16HypCon1_01_A05.CEL
Reading in : WT16HypCon2_02_A07.CEL
Reading in : WT16HypCon3_03_B05.CEL
Reading in : WT16HypInf1_04_B07.CEL
Reading in : WT16HypInf2_05_C05.CEL
Reading in : WT16HypInf3_06_C07.CEL
Reading in : WT16RootCon1_07_D05.CEL
Reading in : WT16RootCon2_08_D07.CEL
Reading in : WT16RootCon3_09_E05.CEL
Reading in : WT16RootInf1_10_E07.CEL
Reading in : WT16RootInf2_11_F05.CEL
Reading in : WT16RootInf3_12_F07.CEL
Reading in : WT26HypCon1_13_H07.CEL
Reading in : WT26HypCon2_14_G07.CEL
Reading in : WT26HypCon3_15_H05.CEL
Reading in : WT26HypInf1_16_G05.CEL
Reading in : WT26HypInf2_17_A05.CEL
Reading in : WT26HypInf3_18_A07.CEL
Reading in : WT26RootCon1_19_B05.CEL
Reading in : WT26RootCon2_20_B07.CEL
Reading in : WT26RootCon3_21_C05.CEL
Reading in : WT26RootInf1_22_C07.CEL
Reading in : WT26RootInf2_23_D05.CEL
Reading in : WT26RootInf3_24_D07.CEL
> eset<-rma(affyRaw,target="core")
Background correcting
Normalizing
Calculating Expression
> featureData(eset)<-getNetAffx(eset,"transcript")
> eset
ExpressionSet (storageMode: lockedEnvironment)
assayData: 38408 features, 24 samples
element names: exprs
protocolData
rowNames: WT16HypCon1_01_A05.CEL WT16HypCon2_02_A07.CEL ...
WT26RootInf3_24_D07.CEL (24 total)
varLabels: exprs dates
varMetadata: labelDescription channel
phenoData
rowNames: WT16HypCon1_01_A05.CEL WT16HypCon2_02_A07.CEL ...
WT26RootInf3_24_D07.CEL (24 total)
varLabels: index
varMetadata: labelDescription channel
featureData
featureNames: 13320001 13320003 ... 13545870 (38408 total)
fvarLabels: transcriptclusterid probesetid ... category (18 total)
fvarMetadata: labelDescription
experimentData: use 'experimentData(object)'
Annotation: pd.aragene.1.1.st
> featureData(eset)
An object of class "AnnotatedDataFrame"
rowNames: 13320001 13320003 ... 13545870 (38408 total)
varLabels: transcriptclusterid probesetid ... category (18 total)
varMetadata: labelDescription
> varLabels(featureData(eset))
[1] "transcriptclusterid" "probesetid" "seqname"
[4] "strand" "start" "stop"
[7] "totalprobes" "geneassignment" "mrnaassignment"
[10] "swissprot" "unigene" "gobiologicalprocess"
[13] "gocellularcomponent" "gomolecularfunction" "pathway"
[16] "proteindomains" "crosshybtype" "category"
> pData(featureData(eset))[1000:1002,]
transcriptclusterid probesetid seqname strand start stop
totalprobes
13321999 13321999 13321999 <na> <na> NA NA
NA
13322001 13322001 13322001 <na> <na> NA NA
NA
13322003 13322003 13322003 <na> <na> NA NA
NA
geneassignment
13321999 --- // --- // intron-exon control // --- // ---
13322001 --- // --- // intron-exon control // --- // ---
13322003 --- // --- // intron-exon control // --- // ---
mrnaassignment
13321999 --- // --- // intron-exon control // --- // --- // --- // ---
//
--- // --- //
13322001 --- // --- // intron-exon control // --- // --- // --- // ---
//
--- // --- //
13322003 --- // --- // intron-exon control // --- // --- // --- // ---
//
--- // --- //
swissprot unigene gobiologicalprocess gocellularcomponent
13321999 NA NA NA NA
13322001 NA NA NA NA
13322003 NA NA NA NA
gomolecularfunction pathway proteindomains crosshybtype
13321999 NA NA NA NA
13322001 NA NA NA NA
13322003 NA NA NA NA
category
13321999 normgene->intron
13322001 normgene->intron
13322003 normgene->intron
>
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