Question: processing illumina signal count
gravatar for arshiaurora
4.9 years ago by
United States
arshiaurora0 wrote:


I have downloaded an available Illumina data set from GSE. say GSExxx_non-normalized.txt. When I open this file I see Ilumina probes and two columnsfor each sample - Sample name and Detection P.val

The values under Sample name are probe intensities I am assuming. And since they range from 200 - 50,000. I am again assuming this is some signal count data. This does not look symmetrical either. How is a typical Illumina data  distribution supposed to look like ? How do I proceed from these signal count data to normalized data ?

example data:

              LSB_D2A Detection.Pval  LSB_D2B Detection.Pval.1  LSB_D2C

ILMN_1762337 132.1310      0.9723320 150.3600        0.5665349 172.1407

ILMN_2055271 160.8341      0.5704875 162.1784        0.3148880 230.9839

ILMN_1736007 163.2743      0.5309618 131.0754        0.9393939 218.1598

ILMN_2383229 174.2183      0.3557312 174.8238        0.1357049 174.4930

ILMN_1806310 179.0533      0.2898551 162.5364        0.3083004 190.7130

ILMN_1779670 162.6389      0.5388669 160.4553        0.3438735 177.7338

Many thanks for your help!

count raw gse process illumina • 1.1k views
ADD COMMENTlink modified 4.9 years ago • written 4.9 years ago by arshiaurora0

As you can see this cannot be processed by R package LUMI as I don't have the necessary BEAD columns. 

ADD REPLYlink written 4.9 years ago by arshiaurora0
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