Ilumina Genome Studio: How to extract control_probe_profile?
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6.9 years ago
elenichri ▴ 20

Dear Biostars community,

I am analyzing a microarray gene expression dataset generated with the Illumina human ht-12 v4 platform. I have loaded the raw image data to Genome Studio and calculated the sample_probe_profile (I am interested in the probe-level measurement). I want to extract the raw data and then use the neqc() function from Bioconductor's limma package for preprocessing. I read at the documentation that, for more accurate results, a file called Control_Probe_Profile is needed. Genome Studio is supposed to extract this under Analysis > Reports > Final Review...However, I cannot see it there. I only see Group and Sample Probe and Gene Profile files (4 in total). Where is the Control_Probe_Profile file located?

Thank you very much for any help!

Eleni

Illumina Genome Studio Controls • 2.2k views
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6.9 years ago

I think you're looking for section 149 here - The Control Probe Profile

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Thank you Andrew. Yes, this is what I am looking for...however, when my analysis is done, I don't see this table in my options (fig 88). It does not appear at the output as well, even when I restore the view to the IGS defaults. Is this possible under any conditions or it means that I did something wrong?

Thank you very much!

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If I remember right (it's been a while) - You need to add fields such as bead std error to the output (just add every field), which is controllable by one of the buttons. You're then looking to export which is another button up there. (sorry I can't be more specific).

What you might find useful is the lumidat package, which takes IDAT files and produces the sample/control probe profiles (along with parameters).

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Thank you Andrew. I will try to find it and if not I will use the lumidat package. I was not aware of that.

Best regards,

Eleni

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