[BioC] oligo and pd.aragene.1.1.st annotation

[Marc Carlson]

Hi Stephen,

It sounds like you might need to make an annotation package for your new 
platform.  You can see a vignette that shows how to do that here:

http://www.bioconductor.org/packages/2.10/bioc/vignettes/AnnotationDbi/inst/doc/SQLForge.pdf

Please let me know if there are any other issues that crop up.


   Marc



On 08/02/2012 09:20 AM, Stephen Rolfe wrote:
> 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
>
>
> 	[[alternative HTML version deleted]]
>
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