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/
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.