[BioC] Detection Above Background (DABG) on Gene Level for Exon and Gene Arrays

Pascal Gellert pascal.gellert at mpi-bn.mpg.de
Tue Sep 21 14:27:28 CEST 2010

Hi all,

The detection above background algorithm calculates a p-value for each 
probe set, indication if this probe set is expressed or not (within the 
background noise).
This is similar to the MAS5 detection calls, but Exon 1.0 ST and Gene 
1.0 ST Arrays don't have mismatch probes, therefore MAS5 cannot be used.

According to Affymetrix, the DABG is not valid on gene level:

"There is a strong assumption in DABG
that all the probes are measuring the same
thing (i.e., the same transcript). This is not
the case at the gene level due to alternative
splicing. For example, probes for a cassette
exon that is skipped will contribute to a mis-
leadingly insignificant p-value."

To obtain, if a gene is expressed, often all probe sets of a gene were 
used. If less than e.g. 50% of the exons of the gene are above a DABG 
threshold, the gene is considered as not expressed.

Nevertheless, the XPS package supports DABG on gene level. Does anyone 
has experiences with DAGB on gene level?


Pascal Gellert

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