Question: filtering out probes with no gene symbol from expressionSet
0
gravatar for alakatos
4.5 years ago by
alakatos100
United States
alakatos100 wrote:

Hello,

apologize if this question was asked before but I did not find an answer to my issue.

I would like to subset my expressionSet choosing the probes only which have gene symbol.

eSet object:

ExpressionSet (storageMode: lockedEnvironment)
assayData: 35556 features, 6 samples 
  element names: exprs 
protocolData: none
phenoData
  sampleNames: GSM1153102 GSM1153103 ... GSM1153107 (6 total)
  varLabels: title geo_accession ... data_row_count (36 total)
  varMetadata: labelDescription
featureData
  featureNames: 10338001 10338002 ... 10608724 (35556 total)
  fvarLabels: ID Symbol Name Ensembl
  fvarMetadata: Column Description labelDescription
experimentData: use 'experimentData(object)'
Annotation: mogene11sttranscriptcluster.db  

 

Thank you for your help.

Anita 

 

ADD COMMENTlink modified 4.5 years ago • written 4.5 years ago by alakatos100
Answer: filtering out probes with no gene symbol from expressionSet
0
gravatar for svlachavas
4.5 years ago by
svlachavas690
Greece/Athens/National Hellenic Research Foundation
svlachavas690 wrote:

What do you mean by the question Gene Symbol ? Do you mean excude probesets that dont match to ENTREZID or there are not annotated ? If so, you could check the genefilter package and the function nsFilter()

Then, you could write something like below:

eset <- nsFilter(eSet, require.entrez=TRUE, remove.dupEntrez=FALSE, var.filter=FALSE, var.cutoff=0.5, feature.exclude="^AFFX")$eset

where you remove probesets without an Entrez Gene ID annotation. 

 

ADD COMMENTlink written 4.5 years ago by svlachavas690
Answer: filtering out probes with no gene symbol from expressionSet
0
gravatar for alakatos
4.5 years ago by
alakatos100
United States
alakatos100 wrote:

Hi,

 

Thanks for your quick reply. Yes, I meant annotation : probesets with Symbol or  Entrezid.  Thanks for the code and the package suggestion. I will look into it.

Thanks once again, 

Anita 

 

 

ADD COMMENTlink written 4.5 years ago by alakatos100

Moreover, regarding annotation, it would make more sense if you have performed statistical inference firstly, you could then filter out missing annotations or duplicates. 

ADD REPLYlink written 4.5 years ago by svlachavas690
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