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bye_nary 01-14-2010 11:56 AM

BeadStudio Output - Quality Control?

I am to receive a human gene expression dataset output but illumina beadstudio. The data comprises of an AVG_DETECTION column and a DETECTION_P for each signal in every person. This p-value represents the probability that the signal was derived from a non-specific probe hybridisation (i.e. noise).

Does anyone have an insight into the best way I can quality control this data WRT the P-values? For example, should I be removing probes from my analysis if a certain number do not exceed a significance threshold of, say, 0.05? or should I be removing people?

Could somone at least point me to a paper that has done this before?

Thanks in advance.

AsbesMesoReality 01-17-2010 03:54 PM

Hi From Italy

Greetings from Italy! Thought I would share somethings I have learned as well as learn from others.

Wish Everyone out here a belated Merry Christmas


Brent1 01-22-2010 04:38 PM

Re: BeadStudio Output - Quality Control?
Hi bye_nary,

You might find the following document helpful in developing your QC strategy for BeadStudio and Gene Expression Data.

illumina website -->
Support / Product Literature -->
Gene Expression Microarray Data Quality Control



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