GEO illumina gene array analysis

Question

[kanwarjag]

I downloaded GSE45002 which is a public illumina gene expression array. However the data only has non-normalized data. How best I can analyze or at least normalized this data. I am sure there should be some method otherwise it is of no use of submitting data to GEO.

Thanks

Answer 1

[h.mon]

The limma user guide is a great resource for someone starting on gene expression microarrays, and covers normalization among many other subjects.

[kanwarjag]

The data is in txt file:

ILMN_3162511    184.6496    0.02506266    164.062
ILMN_3162516    165.2007    0.1867168     170.7453
ILMN_3162526    148.314     0.7456141     165.1285
ILMN_3162536    183.3001    0.02756892    178.0172
ILMN_3162551    145.1749    0.8508772     153.7765
ILMN_3162564    309.0072    0             213.7963

In affy we have cel files in GEO but we don't have anything like this in case of Illumina expression data. So not sure how to process it. I think limma may need more information in addition to raw intensity and there are no bead column and other information is there

[h.mon]

See if this helps.