[ Update: Sorry for the dup. I tried using the new formatting on this one, but found a problem, which I hope is fixed now.]
I promise this is the last one. Here we load the sample data from ExpressionSet. I show (once again) how to obtain all the relevant stuff: expression data, sample names, feature names, and gene names.
One of the nice things about ExpressionSet objects is the very fancy indexing one can do with them. A great example is given on p. 166 of the Bioconductor book.
I made an stab at implementing range selectors here but it's almost trivial. Also, in this one, the Python code does not contain any informative whitespace, so I've used the <code> tag.
The script is first and then the output. If you can't figure something out, just ask.
> python script.py ExpressionSet (storageMode: lockedEnvironment) assayData: 500 features, 26 samples element names: exprs, se.exprs protocolData: none phenoData sampleNames: A B ... Z (26 total) varLabels: sex type score varMetadata: labelDescription featureData: none experimentData: use 'experimentData(object)' Annotation: hgu95av2 Features Samples 500 26  192.742 Features Samples 3 3  "AFFX-MurIL2_at" "AFFX-MurIL10_at" ******* Deprecation warning *******: The package 'hgu95av2' is deprecated and will not be supported in the future. Instead we strongly reccomend that you should start using the 'hgu95av2.db' package. We hope you will enjoy these new packages. If you still have questions, you can search (http://dir.gmane.org/gmane.science.biology.informatics.conductor) or ask the mailing list (http://bioconductor.org/docs/mailList.html). Loading required package: hgu95av2 ['', 'STAT1', 'GAPDH', 'ACTB', 'TFRC'] ['C15orf31', 'ACTL6B', 'GLRA1', 'KCNB2', 'MGAT5'] ['BMP3', 'RPL14', 'ZCWPW2', 'KITLG', 'GPR12'] ['TRA@', 'ATP8A2', 'C1orf68', 'FAM20B', 'SLC34A1'] sex type score A Female Control 0.75 B Male Case 0.40 C Male Control 0.73 >