analysis of normalised data in bioconductor

Question

[Sabine]

I have analysed few affymetrix CEL fiiles, then prepared normalised data as excel using Bioconductor.

Now I would like to know how I can determine the possible list of genes from that. I have used 2 methods for the normalization, namely RMA and mas5

[Devon Ryan]

You'll want to stay within R rather than going to Excel.

Which microarray exactly? There are annotation files for most of the common ones in Bioconductor.

[Sabine]

How can I get those annotation files?

[Devon Ryan]

Have a look at, for example, this page. Find the appropriate package for the array you used, click on its page and follow the installation instructions. There are also usage instructions there as well, though you may or may not find them very informative (they're not always that geared toward absolute beginners, unfortunately).

[Sabine]

I have installed this through this command in bioconductor earlier itself

biocLite("hgu133plus2.db")

[Devon Ryan]

Then you can use the hg133plus2ALIAS2PROBE object. Have a read through the AnnotationDbi "how to" for more useful usage examples.

[Sabine]

I had been analysing the CEL files using altanalyse. but could not find proper results

These are the parameters I have used.

method : moderated t-test

considered adj pvalue and fold change 2 , which is default in altanalyse

any suggestions please?

Answer 1

[David Westergaard]

Check out this past tutorial on how to analyse Affymetrix data.