[BioC] Detection Above Background (DABG) on Gene Level for Exon and Gene Arrays
pascal.gellert at mpi-bn.mpg.de
Tue Sep 21 14:27:28 CEST 2010
The detection above background algorithm calculates a p-value for each
probe set, indication if this probe set is expressed or not (within the
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?
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