Question: Analysing illumina micro array
0
gravatar for rohit
4.1 years ago by
rohit30
India
rohit30 wrote:

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  

 

illumina R non normalized • 1.9k views
ADD COMMENTlink modified 4.1 years ago by andrew.j.skelton735.8k • written 4.1 years ago by rohit30
0
gravatar for andrew.j.skelton73
4.1 years ago by
London
andrew.j.skelton735.8k wrote:

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. 

ADD COMMENTlink written 4.1 years ago by andrew.j.skelton735.8k
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