[BioC] topTable (fit) annotation
Jing Huang
huangji at ohsu.edu
Wed Aug 31 18:50:56 CEST 2011
Sorry. My problem is the colnames(topTable(fit)) that I generated by GEO
GSE dataset only provides a few items such as pValue...
I would like to have a full table just like GEO GDS dataset generated. I
describe the problem at my original email: Different dataset of GEO
provides different patten on topTable(fit).
This generated with GDS dataset
>colnames(topTable(fit))
[1] "ID" "Gene.title" "Gene.symbol"
[4] "Gene.ID" "UniGene.title" "UniGene.symbol"
[7] "UniGene.ID" "Nucleotide.Title" "GI"
[10] "GenBank.Accession" "Platform_CLONEID" "Platform_ORF"
[13] "Platform_SPOTID" "Chromosome.location"
"Chromosome.annotation"
[16] "GO.Function" "GO.Process" "GO.Component"
[19] "GO.Function.1" "GO.Process.1" "GO.Component.1"
[22] "CTRL" "HIF1a" "HIF2a"
[25] "HIF1a2a" "AveExpr" "F"
[28] "P.Value" "adj.P.Val"
This generated with GSE dataset
>colnames(topTable(fit)
[1] "ID" "mir210" "CTRL2" "AveExpr" "F"
"P.Value" "adj.P.Val"
I hope this is clear.
Jing
On 8/31/11 9:38 AM, "Freudenberg, Johannes (NIH/NIEHS) [E]"
<johannes.freudenberg at nih.gov> wrote:
>Hi Jing,
>
>I'm not quite sure I understand your question. Why can't you use the
>data for further analysis? Maybe the issue is that getGEO() returns a
>list? Have you tried something like:
>
>> gse16962 <- getGEO("GSE16962")
>> eset <- gse16962[[1]]
>> head(fData(eset))
> ID GB_ACC SPOT_ID Species.Scientific.Name Annotation.Date
>1007_s_at 1007_s_at U48705 <NA> Homo sapiens Mar 11, 2009
>1053_at 1053_at M87338 <NA> Homo sapiens Mar 11, 2009
>117_at 117_at X51757 <NA> Homo sapiens Mar 11, 2009
>121_at 121_at X69699 <NA> Homo sapiens Mar 11, 2009
>1255_g_at 1255_g_at L36861 <NA> Homo sapiens Mar 11, 2009
>1294_at 1294_at L13852 <NA> Homo sapiens Mar 11, 2009
> Sequence.Type Sequence.Source
>1007_s_at Exemplar sequence Affymetrix Proprietary Database
>1053_at Exemplar sequence GenBank
>117_at Exemplar sequence Affymetrix Proprietary Database
>121_at Exemplar sequence GenBank
>1255_g_at Exemplar sequence Affymetrix Proprietary Database
>1294_at Exemplar sequence GenBank
>
>Etc.
>
>--Johannes
>
>
>
>-----Original Message-----
>From: Jing Huang [mailto:huangji at ohsu.edu]
>Sent: Wednesday, August 31, 2011 12:21 PM
>To: Davis, Sean (NIH/NCI) [E]
>Cc: bioconductor at r-project.org
>Subject: Re: [BioC] topTable (fit) annotation
>
>Thank YOU Sean for responding my question. I am not sure where I should
>add the platform annotation in.
>
>Here are what I observed:
>
>If I extract "GDS2162" by typing in
>
>> gds=getGEO("GDS2162")
>> eset=GDS2eSet(gds,do.log2=T)
>
>>eset
>
>ExpressionSet (storageMode: lockedEnvironment)
>assayData: 45101 features, 16 samples
> element names: exprs
>protocolData: none
>phenoData
> sampleNames: GSM67339 GSM67343 ... GSM67352 (16 total)
> varLabels: sample genotype/variation agent description
> varMetadata: labelDescription
>featureData
> featureNames: 1415670_at 1415671_at ... AFFX-TrpnX-M_at (45101 total)
> fvarLabels: ID Gene.title ... GO.Component.1 (21 total)
>
> fvarMetadata: Column labelDescription
>experimentData: use 'experimentData(object)'
> pubMedIds: 16237459
>Annotation:
>
>Most of annotation is in.
>
>
>
>If I extract "GSE16962" by typing in
>
>>gse=getGEO("GSE16962")
>
>> gse
>$GSE16962_series_matrix.txt.gz
>ExpressionSet (storageMode: lockedEnvironment)
>assayData: 54675 features, 12 samples
> element names: exprs
>protocolData: none
>phenoData
> sampleNames: GSM424759 GSM424760 ... GSM424770 (12 total)
> varLabels: title geo_accession ... data_row_count (34 total)
> varMetadata: labelDescription
>featureData
> featureNames: 1007_s_at 1053_at ... AFFX-TrpnX-M_at (54675 total)
> fvarLabels: ID GB_ACC ... Gene.Ontology.Molecular.Function (16 total)
> fvarMetadata: Column Description labelDescription
>experimentData: use 'experimentData(object)'
>Annotation: GPL570
>
>It looks to me it includes annotation package such as GO term....
>But I can't use this eset data to do further analysis (such as fit table)
>what I need.
>
>If I extract ("GSE16962") by typing in
>
>>gse=getGEO("GSE16962", GSEMatrix=F)
>
>Then following GEOquery package, I can generate eset2, which I can use to
>do analysis what I need. But the eset2 looks like this:
>
>> eset2
>ExpressionSet (storageMode: lockedEnvironment)
>assayData: 54675 features, 12 samples
> element names: exprs
>protocolData: none
>phenoData
> sampleNames: GSM424759 GSM424760 ... GSM424770 (12 total)
> varLabels: samples
> varMetadata: labelDescription
>featureData: none
>experimentData: use 'experimentData(object)'
>Annotation:
>
>
>
>Here are the scripts that I use to generate eset2:
>
>>probesets <- Table(GPLList(gse)[[1]])$ID data.matrix <-
>>do.call("cbind", lapply(GSMList(gse), function(x) {
>+ tab <- Table(x)
>+ mymatch <- match(probesets,tab$ID_REF)
>+ return(tab$VALUE[mymatch])
>+ }))
>> data.matrix <- apply(data.matrix, 2, function(x) {
>+ as.numeric(as.character(x))
>+ })
>> require(Biobase)
>> rownames(data.matrix) <- probesets
>> colnames(data.matrix) <- names(GSMList(gse)) pdata <-
>> data.frame(samples=names(GSMList(gse)))
>> rownames(pdata) <- names(GSMList(gse)) pheno <-
>> as(pdata,"AnnotatedDataFrame")
>> eset2 <- new('ExpressionSet',exprs=data.matrix,phenoData=pheno)
>
>
>At which step, I should add
>
>>gplannot = getGEO("GPL96", AnnotGPL=TRUE)
>
>
>Many Many thanks
>
>Jing
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>On 8/30/11 6:01 PM, "Sean Davis" <sdavis2 at mail.nih.gov> wrote:
>
>>Hi, Jing.
>>
>>NCBI GEO maintains two types of GPL records. The normal variant is
>>just supplied by the submitter. However, when a GEO Series is curated
>>by NCBI GEO into a GEO DataSet (GDS), they create a so-called
>>"Annotation GPL". These have a relatively standard set of columns. I
>>have not made the change to GEOquery yet to grab this annotation GPL
>>when getting Series Matrix files. But, you can get them yourself by
>>specifying:
>>
>>gplannot = getGEO("GPL96", AnnotGPL=TRUE)
>>
>>You can always replace the feature data of the ExpressionSets with the
>>information in the retrieved Annotation GPL.
>>
>>I hope that is clear.
>>
>>Sean
>>
>>
>>On Tue, Aug 30, 2011 at 5:01 PM, Jing Huang <huangji at ohsu.edu> wrote:
>>> Dear All members,
>>>
>>> I have been extracting data from GEO (GEO package) and do some
>>>analysis on them by using limma package. What I discover is the
>>>components of
>>>topTable(fit) are different from the dataset GDS and GSE.
>>>
>>> If the data is from GDS, then the colnames of topTable (fit) looks
>>>like this.
>>>
>>>> colnames(topTable(fit))
>>> [1] "ID" "Gene.title" "Gene.symbol"
>>> [4] "Gene.ID" "UniGene.title" "UniGene.symbol"
>>> [7] "UniGene.ID" "Nucleotide.Title" "GI"
>>> [10] "GenBank.Accession" "Platform_CLONEID" "Platform_ORF"
>>> [13] "Platform_SPOTID" "Chromosome.location"
>>>"Chromosome.annotation"
>>> [16] "GO.Function" "GO.Process" "GO.Component"
>>> [19] "GO.Function.1" "GO.Process.1" "GO.Component.1"
>>> [22] "CTRL" "HIF1a" "HIF2a"
>>> [25] "HIF1a2a" "AveExpr" "F"
>>> [28] "P.Value" "adj.P.Val"
>>>
>>> If the data is from GSE, then the colnames of topTable(fit) looks
>>>like this:
>>>
>>>>colnames(topTable(fit)
>>>
>>> [1] "ID" "mir210" "CTRL2" "AveExpr" "F"
>>>"P.Value" "adj.P.Val"
>>>
>>> I am trying to add some term into this table by doing following one
>>>by
>>>one: the data is generated by Affymetrix human U133 platform:
>>>
>>>>Library(hgu133plus2.db)
>>>>x=hgu133plus2SYMBOL
>>>>y=topTable(fit)
>>>>y$SYMBOL=unlist(as.list(x[y$ID]))
>>>
>>> It works but I need to add ENTREZID,SYMBOL,CHR, CHRloc, and GO
>>>annotations as well. I like to have the topTable more like the
>>>topTable(fit) generated at top by data GEO GDS data
>>>
>>> I am wondering if there is an easy way to annotate all once.
>>>
>>> In addition, I am having a trouble to annotate GO term.
>>>
>>> Many Thanks
>>>
>>> Jing
>>>
>>>
>>>
>>>
>>> [[alternative HTML version deleted]]
>>>
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>
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