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michael watson IAH-C
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@michael-watson-iah-c-378
Last seen 10.1 years ago
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
Mick