Hello everyone,
I am tasked with analysing the gene expressions from Illumina microarray. I've downloaded Illumina raw data and non- normalized data from GEO having accession number GSE31738. In the raw data folder I couldn't find any text file having Average signal, BEAD_STDERR and Average NBEADS but in non-normalized file I found detection and P values. Is it possible to get the expression values with detection and P values?
I have analysed with GEO2R but I found that some sample values are like 2450.2, 2785, 4056 etc.
Below table is from the non- normalized data file.
Can anyone please help me in analysing this illumine microarray/
Thanking You in advance
Non-normalized data:
ID_REF MSC_1Detection Pval MSC_2Detection Pval MSC_3Detection Pval
ILMN_2735294 130.6 0.81659 149.5 0.94216 137.8 0.87029
ILMN_2417611 101.6 0.08734 105.6 0.12013 112.6 0.34701
ILMN_2730714 11644 1.000 13630.4 1.000 12601.7 1.00000
ILMN_2543688 4827.1 1.000 4720.2 1.000 6739.3 1.000
1 answer
As with all GEO entries, it depends on how thorough the submitter was. If you want bead level information, then you'd need a sample probe profile, or the IDAT files. Uploading IDAT files is completely optional, so the data you've got could be coerced into a lumi batch object (I think) - You've got raw expression and a detection P value. I suggest you take a look at the GEOQuery package.
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andrew.j.skelton73
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