[BioC] fold-change when no expression to high expression

Matthew McCormack mccormack at molbio.mgh.harvard.edu
Thu May 28 00:02:26 CEST 2009

Transcripts not expressed in control but which have high expression in 
treatment theoretically have an infinite fold-change. Preprossesing 
algorithms will provide numbers for fold-change for these genes, but to 
do this there seems to be an assumption that all genes are expressed to 
some small degree at all times and that the chip can reliably detect 
this. If this is not the case, then it would seem that the fold-change 
number the preprocessing algorithms provide for genes that go from no 
expression to expression would be very unreliable and would not be able 
to be compared with fold changes for other genes that have an 
appreciable signal intensity in both control and treatment. These genes, 
off-on genes, are biologically very important to identify. Not 
identifying these genes because of the low or no control signal 
intensity would provide misleading data from a biological viewpoint. Is 
there any algorithm on BioConductor that addresses this problem ?

Matthew McCormack

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