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

[Laurent Gautier]

If I understand your question right, the issue is about fold-changes for 
which the denominator is very small/zero.

You may consider adding a small offset to the signal ("fudge factor") 
making the denominator leave the "danger zone", or using a 
generalized-log transform (I think that the function glog() is in the 
package "vsn").


L.


Matthew McCormack wrote:
> 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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