Question: How to exclude columns of phenoData of ExpressionSet Data in R
0
gravatar for floodking
3.9 years ago by
floodking0
floodking0 wrote:

I want to select columns from phenoData of ExpressionSet in R. My data to be processes is teset.

class(teset)
[1] "ExpressionSet"
attr(,"package")
[1] "Biobase"

teset
ExpressionSet (storageMode: lockedEnvironment)
assayData: 19420 features, 253 samples 
 element names: exprs
   protocolData: none
phenoData
  sampleNames: TCGA-CV-7091-01A-11D-2012-08 TCGA-CJ-4875-01A-01D-1373-10 ...
    TCGA-25-1626-01A-01W-0615-10 (253 total)
  varLabels: time status ... Tumor_grade (7 total)
  varMetadata: labelDescription
featureData
  featureNames: 1060P11.3 A1BG ... ZZZ3 (19420 total)
  fvarLabels: EntrezID Symbol Desc Synonyms
  fvarMetadata: labelDescription
 experimentData: use 'experimentData(object)'
Annotation:  

covariates information of teset:

names(pData(teset))
[1] "time"            "status"          "Age"             "Gender"         
[5] "TCGA_tumor_type" "Tumor_stage"     "Tumor_grade"

I only want a teset data without the first two columns in pData, namely all exprs data with pData(teset)[,-c(1,2)]. How can I do this? Thanks for help!!!

expressionset biconductor R • 1.7k views
ADD COMMENTlink written 3.9 years ago by floodking0

You don't need to change or exclude anything, just don't include those terms in your model.

ADD REPLYlink written 3.9 years ago by Devon Ryan91k

How to achieve this?

ADD REPLYlink written 3.9 years ago by floodking0
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