I'm trying to do DEG analysis on a dataset from ArrayExpress, E-GEOD-38628. This data is from an Affymetrix 1.0 ST array. The documentation of ArrayExpress() says:
"The output is an object of class ‘AffyBatch’ or ‘ExpressionSet’ or
‘NChannelSet’ with the raw expression values in the assayData of
the object, the information contained in the .sdrf file in the
phenoData, the adf file in the featureData and the idf file
content in the experimentData."
The actual output of ArrayExpress("E-GEOD-38628") is a FeatureSet.
... E-GEOD-38628 was successfully loaded into GeneFeatureSet > mydata.raw GeneFeatureSet (storageMode: lockedEnvironment) assayData: 1102500 features, 14 samples
This prevents me from doing GCRMA on this data.
Error in (function (classes, fdef, mtable) :
unable to find an inherited method for function ‘indexProbes’ for signature ‘"GeneFeatureSet", "character"’
Why is ArrayExpress giving me a FeatureSet instead of an AffyBatch?
Can I make ArrayExpress give me an AffyBatch instead?
Should I just use the FeatureSet instead?
What does FeatureSet do that AffyBatch doesn't?
How can I run gcrma() on this data?
What documentation should I have read to understand these issues going in?
Thanks for any insight you can provide.