Analysing illumina micro array

Question

[rohit]

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

<caption>non normalized data</caption>

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

 

Answer 1

[andrew.j.skelton73]

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.