Entering edit mode
8.6 years ago
floodking
•
0
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!!!
You don't need to change or exclude anything, just don't include those terms in your model.
How to achieve this?