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GEO illumina gene array analysis

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

gene-array illumina geo
• 2,633 views • link
updated by Ram Ram • written by kanwarjag kanwarjag

1 answer

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

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updated by Ram Ram • written by h.mon h.mon

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

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updated by Ram Ram • written by kanwarjag kanwarjag

See if this helps.

• 1 views • link
updated by Ram Ram • written by h.mon h.mon

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