Getting Raw illumina microarray data from GEO

Question

[giroudpaul]

Hi

I want to analyze some publicly available Dataset one GEO, that uses the IlluminaHuman12 v4 beadarray (such as GSE49240)

Using gse <- getGEO("GSE49240"), it downloaded GSE49240_series_matrix.txt.gz.

However, I understood from GEOquery vignette that the RAW data should be accessed with getGEOSuppFiles.

Then, what are the data I got with getGEO ? Normalized data ? How have they been normalized ?

What should I use if I want to perform the normalization and QC analysis myself (using lumi or beadarray) ?

Thanks

[venu]

Then, what are the data I got with getGEO ? Normalized data ? How have they been normalized ?

Most of the times (if not, in my experience) the normalized data is deposited in GEO. In the relevant paper they must discuss 'How they have normalized the data and analysed'. If you want to get the raw data, you can consult the authors requesting for the raw data.

Answer 1

[igor]

If you check the GEO record (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE49240), it doesn't look like the raw data is actually there.

With GEO, you don't always know what you get. Different people submit different types of files.

[giroudpaul]

So how I am supposed to deal with the data available ? Perform QC and see if it's already ok and then proceed with limma DE analysis seems reasonable ?

[igor]

Just be really careful to make sure the data is what you think it is (as far as normalization goes). You can also see what GEO2R does.