[BioC] Ringo package: error using computeRunningMedians function

[Joern Toedling]

Hello,

I'm afraid I do not understand the error message. NAs in your ExpressionSet
should not be a problem. I suspect that the problem might be with your
probeAnno object, especially with the probes on chromosome 11 (since it seems
to work with chromosomes 1 and 10). How did you build the probeAnno object? 
Assuming your probeAnno object is called P,
what is the output of 
validObject(P)
str(P["11.start"])
str(P["11.index"])
? And please always remember to add the result of typing "sessionInfo()" in
your R to any question you ask on this list, as this allows us to see which
software versions you are using.

Regards,
Joern

On Mon, 31 Aug 2009 11:48:17 +0000, Diego Villar wrote
> Dear All,
> 
>   I am trying to use Ringo for analysis of Agilent platform ChIP-
> chip. I get the following output/error when applying the computeRunningMedians
> function to my expression set (2 samples, one normal and one dye-
> swap):
> 
>   Chromosome 1 ...
> 170809ds ... 261108no ...
> Chromosome 10 ...
> 170809ds ... 261108no ...
> Chromosome 11 ...
> 170809ds ... Error en newExprs[chridx, i] <- chrrm :
>   NAs are not allowed in subscribed assignations
> 
>    Does this mean missing values are not allowed at all for this
> function? How could I modify my input so that the function would 
> work on my data? Would I need to substite NAs somehow in the ExpressionSet?
> 
>    Thanks in advance for your time and help,
> 
>                 Diego Villar
> 


---
Joern Toedling
Institut Curie -- U900
26 rue d'Ulm, 75005 Paris, FRANCE
Tel. +33 (0)156246926