Monthly Archives: October 2013

R/Bioconductor package installation on Ubuntu: Error messages

I fixed this issue by starting R as root user, then installing the necessary packages. Apparently, this was a common rookie mistake using R and Ubuntu/Linux that I luckily searched for and learned about. When installing new R packages in … Continue reading

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Replicate Analyses

This is a good exercise/assignment to replicate published analyses: http://bioinformatics.risha.me/r/ http://www.stjuderesearch.org/site/data/AML1/

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ExpressionSet success!!

Behold, the ExpressionSet object: > sponge_ExpressionSet<-new(“ExpressionSet”,exprs=sponge_data,phenoData=pd,experimentData=experimentData,featureData=an)> sponge_ExpressionSet ExpressionSet (storageMode: lockedEnvironment) assayData: 15744 features, 72 samples element names: exprs protocolData: none phenoData sampleNames: 1_1 1_2 … 9_8 (72 total) varLabels: Chip Number File Name … Name (9 total) varMetadata: labelDescription featureData … Continue reading

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Py Biobase

This could be useful: http://pydoc.net/Python/rpy2-bioconductor-extensions/0.2-dev/bioc.biobase/

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Error in validObject(.Object)

Biobase’s  “ExpressionSet” package: sponge_ExpressionSet<-new(“ExpressionSet”,exprs=sponge_data,phenoData=pd,experimentData=experimentData,featureData=an) Error in validObject(.Object) : invalid class “ExpressionSet” object: 1: featureNames differ between assayData and featureData invalid class “ExpressionSet” object: 2: sampleNames differ between assayData and phenoData It is looking for the same data in all sets … Continue reading

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