4.0 years ago by
Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
This question apparently relates to Daniel Swan's 2011 tutorial about using the simpleaffy and limma packages to analyse Affymetrix microarray data:
Exactly the same question has been asked elsewhere on this site:
Annotating the results with associated gene symbols
The reason why Daniel Swan's code doesn't run exactly as is because the limma topTable now (in response to user requests) puts the probe IDs into the rownames of the output table rather than into a column called "ID". You can easily see this for yourself just by looking at the top table. So you just have to use rownames(probe.list) instead of probe.list$ID.
Alternatively you could follow the case study (Section 17.2) in the limma User's Guide, which is somewhat better because it puts the gene symbols in the data object right at the beginning of the analysis pipelline instead of the adding them later after the top table has been produced.