Hi Alexandra,

This is a common question, so I'm copying the Bioconductor mailing list.

The background log-2 expression for SCAN is centered at 0 with a standard deviation around 1. This means that that ~95% of the probes measuring background (~80% on the ST array) should have values between -2 and 2. Then the probes measuring signal should be in the 1+ range. So what you should see is a right skewed distribution with values between -2 and say 4 or 5. This is totally expected and normal behavior for SCAN.

Furthermore, negative values mean that the probe's expression was below the expected background estimate. Likely this means that the probe is only measuring background noise and not relevant gene expression.

Regards,
-Steve


From: Alexandra Muñoz <abm362@nyu.edu<mailto:abm362@nyu.edu>>
Date: Thursday, October 11, 2012 Thu, Oct 11, 2011 1:28 PM
To: Stephen Piccolo <stephen.piccolo@hsc.utah.edu<mailto:stephen.piccolo@hsc.utah.edu>>
Subject: Expression Values for SCAN.UPC?

Dear Stephen,

I am working with the SCAN function in your package and have a few questions that I would appreciate if you could answer.  I am concerned about the format of the expression values I have generated and am unclear as to whether I am using the function correctly.

 All of my expression values for samples normalized with this function are highly compressed between the range of -1-3 approximately.   Is this normal for your process? What type of expression values does your function produce(log2,log10,..)?  Why are there negative values?

I have included the script I used as well as expression values generated using RMA and the SCAN function.   These were performed on an Affymetrix 1.0 ST array.

Thank you for your time.

Best,
Alexandra





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