processing illumina signal count
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8.1 years ago
arshiaurora ▴ 10

Hi,

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


count raw process gse illumina • 1.6k views
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As you can see this cannot be processed by R package LUMI as I don't have the necessary BEAD columns.