Thanks Stephen for the clear and reproducible example!
The problem is that columns of pData need to have associated
descriptions in varMetadata, so after your change
> validObject(expressionSet, complete=TRUE)
Error in validObject(expressionSet, complete = TRUE) :
invalid class "ExpressionSet" object: In slot "phenoData" of
class
"AnnotatedDataFrame":
All AnnotatedDataFrame pData column names must be present as rows in
varMetadata, and vice versa
A safer way to do what you want is, for instance,
> expressionSet[["newCol"]] <- sub("rol", "", expressionSet[["type"]])
> phenoData(expressionSet)
sampleNames: A, B, ..., Z (26 total)
varLabels and varMetadata:
sex: Female/Male
type: Case/Control
score: Testing Score
newCol: NA
> validObject(expressionSet, complete=TRUE)
[1] TRUE
(you could also use '$' on expressionSet) To actually provide meaning
metadata requires an additional step
> varMetadata(expressionSet)["newCol", "labelDescription"] <-
+ "My new column"
though we'd like to make that simpler...
It might still be useful in some circumstances to assign using pData,
e.g., when not creating a new column, and doing several manipulations
in sequence, a strategy might be to extract pData, manipulate the date
frame, and reassign.
Hope that helps,
Martin
Edwards.Stephen at epamail.epa.gov writes:
> When running the following code to update the phenoData for my
eset, the
> resulting eset object works fine for downstream analysis. However,
when I
> try to subset the eset, I get the error noted just above the
sessionInfo.
> Am I doing something wrong in the assignment, or should I not assign
using
> the pData method? This usage is still documented, so I assumed it
was
> safe. I know I'm getting some warning messages with the
expressionSet in
> the example, but I get the same error when trying to subset a real
dataset
> created using ReadAffy() and rma() without the corresponding
warnings.
>
>> data(sample.exprSet)
>> expressionSet <- as(sample.exprSet,"ExpressionSet")
> Warning messages:
> 1: The phenoData class is deprecated, use AnnotatedDataFrame (with
> ExpressionSet) instead
> 2: The phenoData class is deprecated, use AnnotatedDataFrame (with
> ExpressionSet) instead
>> isCurrent(expressionSet)
> R Biobase eSet ExpressionSet
> TRUE TRUE TRUE TRUE
>>
>> expressionSet[1:10,c(2,4,10)]
> ExpressionSet (storageMode: lockedEnvironment)
> assayData: 10 features, 3 samples
> element names: exprs, se.exprs
> phenoData
> rowNames: B, D, J
> varLabels and varMetadata:
> sex: Female/Male
> type: Case/Control
> score: Testing Score
> featureData
> rowNames: AFFX-MurIL2_at, AFFX-MurIL10_at, ..., AFFX-BioDn-5_at
(10
> total)
> varLabels and varMetadata: none
> experimentData: use 'experimentData(object)'
> Annotation [1] "hgu95av2"
>>
>> p <- cbind (pData(expressionSet), sub("rol", "",
> pData(expressionSet)$type))
>> names(p)[4] <- "type2"
>> pData(expressionSet) <- p
>> expressionSet[1:10,c(2,4,10)]
> Error in `row.names<-.data.frame`(`*tmp*`, value = c("sex", "type",
> "score", :
> invalid 'row.names' length
>>
>> sessionInfo()
> R version 2.5.0 (2007-04-23)
> i386-pc-mingw32
>
> locale:
> LC_COLLATE=English_United States.1252;LC_CTYPE=English_United
> States.1252;LC_MONETARY=English_United
> States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252
>
> attached base packages:
> [1] "tools" "stats" "graphics" "grDevices" "utils"
"datasets"
>
> [7] "methods" "base"
>
> other attached packages:
> affy affyio Biobase limma
> "1.14.0" "1.4.0" "1.14.0" "2.10.0"
>>
>
> ----------------------------------------
> Stephen W. Edwards, Ph.D.
> Systems Biologist, ADHIO, NHEERL, ORD, USEPA
> U.S. Environmental Protection Agency (B305-01)
> 109 TW Alexander Drive
> Research Triangle Park, NC 27711
> Ph#: 919/541-0514 FAX#: 919/685-3221
>
>
> [[alternative HTML version deleted]]
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
>
https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives:
http://news.gmane.org/gmane.science.biology.informatics.conductor
--
Martin Morgan
Bioconductor / Computational Biology
http://bioconductor.org
