[BioC] RE: Errors with -Inf

michael watson (IAH-C) michael.watson at bbsrc.ac.uk
Fri Sep 17 15:03:00 CEST 2004

Sorry, useless e-mail program.....


This is obviously a wider problem, I think, than simply within limma,
where I found it.

The command:

> imageplot(log2(RG$Rb[,8]), RG$printer, low="white", high="red")

Produces the error:

Error in image.default(0:(gr * sr), 0:(gc * sc), z, zlim = zlim, col =
col,  : 
        invalid z limits

All my other arrays work fine.  The only difference here is that in
array 8, some of the values for Rb are zero.

> summary(RG$Rb[,8])
   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
   0.00   37.00   39.00   39.48   42.00   76.00 

So therefore:

> summary(log2(RG$Rb[,8]))
   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
   -Inf   5.209   5.285    -Inf   5.392   6.248 

R calculates my average log2(Rb) as being -Inf, which I'm guessing is
whats screwing up the imageplot() function.

So, um, any ideas what to do about this?  Estimates of background that
are zero must be pretty rare, but that's the data I have and I don't see
that it is necessarily invalid....


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