[BioC] Removing data already read in.... limma and marrayInput

michael watson (IAH-C) michael.watson at bbsrc.ac.uk
Wed Aug 6 15:13:08 MEST 2003

Hi Guys

Rather an odd title, but here goes...

Basically I have read in my data in both limma (using read.maimages) and marrayInput (using read.marrayRaw).  

I want to normalize my data using loess normalisation, however using both packages (maNorm() and normalizeWithinArrays() methods) I get the error that I have mentioned before on this list:

Error in simpleLoess(y, x, w, span, degree, parametric, drop.square, normalize,  : 
        NA/NaN/Inf in foreign function call (arg 1)
In addition: There were 50 or more warnings (use warnings() to see the first 50)

The problem being that the whole thing bombs out and nothing has been saved, so I make no progress.  NB just as an aside, using maNorm() and "echo=TRUE" I can see how far maNorm() has got before bombing out;  with normalizeWithinArrays() I can't :-(  

I have 60 arrays in my raw data set - reading them in took a lot of time, and normalising them takes a lot of time.  But basically one or more of my arrays is causing R's simpleLoess() function to bomb out, and thus I can't normalise my data.

Now through a process of elimination I can probably figure out with array(s) are causing the problem, so is there a way of "removing" that array from the objects I have already created using read.maimages() and read.marrayRaw()?  Or is it a case of eliminating the bad ones and then re-reading all the data in?  

And does anyone have any idea why I am getting the above error??

Thanks in advance for your help :-D


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