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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