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

[Benilton Carvalho]

and getNetAffx returns whatever Affymetrix provides with their
annotation files... These are quite new arrays, so it's likely that on
future releases they'll add more information. b

On 2 August 2012 18:33, Marc Carlson <mcarlson at fhcrc.org> wrote:
> 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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