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

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

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.