[BioC] LPE error caused by gcRMA [Error invar.M.adap[i] <- ifelse(!is.na(var.M.adap[i - 1]), mean(var.M.adap[i + : replacement has length zero]

[charliew]

Hi Richard,
The error went away when I added a small random number to every value  
in the data and re-ran LPE.

charlie
On Nov 5, 2008, at 5:57 AM, Richard Pearson wrote:

> Wolfgang
>
> I agree with you completely. I'm not suggesting adding random noise  
> will remove any real problem, I'm just suggesting Charlie could do  
> this to see whether his hypothesis about the equal values causing  
> the problem is correct. Personally I think adding random noise  
> should be avoided in any real analysis.
>
> Richard.
>
>
> Wolfgang Huber wrote:
>> 04/11/2008 12:48 Richard Pearson scripsit
>>> Charlie
>>>
>>> Following on from what Guido has said, you could test your  
>>> hypothesis
>>> that the identical values produced by the newer version of gcrma  
>>> are the
>>> problem by adding a small amount of random noise to the gcrma  
>>> expression
>>> values and repeating the LPE analysis. I'm not familiar with LPE  
>>> myself,
>>> but have seen similar problems due to the identical values  
>>> produced by
>>> gcrma with other methods.
>>>
>> Wait a minute ... the raw intensities of one probe vary randomly  
>> across
>> arrays. Most normalisation methods remove some of this variation (the
>> systematic part), while some remains. Now we have a method that -for
>> some probes- totally removes this variation, and provides identical
>> estimates across arrays.
>> Simply adding artificial noise (from which distribution?) won't solve
>> any real problem.
>> Best wishes
>> Wolfgang
>> ------------------------------------------------------------------
>>


----------------------------------------------------------------------------
Charlie Whittaker, Ph.D.
Bioinformatics and Computing Core Facility
The David H. Koch Institute for Integrative Cancer Research At MIT
77 Mass Ave E18-366
Cambridge, MA 02139

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