[BioC] GC-RMA - interpretation of the expression levels

Susan Hilsenbeck sgh at breastcenter.tmc.edu
Fri Jun 10 14:47:27 CEST 2005


Affymetrix chips are "one-color" experiments, so the expression you
refer to is NOT the log-ratio of expression of experimental compared to
reference that you see in "two-color" cDNA experiments. Affy expression 
is an "absolute expression, in the sense
that high numbers mean more molecules and low numbers mean few
molecules, although the numbers can only be compared within gene and
cannot be compared between genes (i.e. if one gene has a higher number
than another, that does not necessarily mean that the first gene had
more molecules).


Pintilie, Melania wrote:

>Hello everyone,
>I am a statistician at the Ontario Cancer Institute. Recently, I had to
>analyse an affymetrix dataset. The data have been normalized and the level
>expressions were calculated using GC RMA as implemented in R.
>My role is to analyse the expression levels (which were calculated using GC
>RMA) using SAM and other statistical techniques.
>The expression levels which were given to me (calculated with GC RMA) are
>very large: all are >1. I wonder if this is what one would expect. The
>analyst assures me that a log transformation was also applied.
>I am not sure how to interpret this numbers. What would be the levels of:
>'not expressed', 'over expressed', or 'under expressed'?
>For example I know that the expression levels (not logged) obtained using
>cDNA microarray can be interpreted (ideally)as: 1=no expression, >2 over
>expression and <0.5 under expression.
>I appreciate your help.
>Thank you.
>Melania Pintilie
>Biostatistics Department
>Ontario Cancer Institute
>University of Health Network/Princess Margaret Hospital
>Toronto, M5G 2M9
>Tel: (416) 946-4501 ext. 4886
>Fax: (416) 946-2048
>Bioconductor mailing list
>Bioconductor at stat.math.ethz.ch

Susan Galloway Hilsenbeck, PhD........mailto:sgh at breastcenter.tmc.edu
Breast Center at Baylor College of Medicine... MaBell: (713) 798-1627
One Baylor Plaza, MS BCM600................... Fax: (713) 798-1642
Houston, TX 77030

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