Entering edit mode
Dear Mick,
At 11:13 PM 6/08/2003, michael watson (IAH-C) wrote:
>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:
Obviously I would like to get to the bottom of this.
First point: I did a lot of work about a month and half ago to speed
up the
loess normalization in limma considerably. As a result, limma no
longer
makes any calls to loess (which is the function which calls
simpleLoess),
unless you are using method="composite". Can you ask you to install
the
development version of limma and see if you still get an error (quite
likely you will).
Secondly: you haven't given use anything like enough information to
solve
any problems. You haven't told us the calling sequence you used, which
normalization method was invoked et etc. In order to help us help you,
you
need to (i) try to isolate the problem by finding the smallest data
set
which will reproduce the error and (ii) show us the whole calling
sequence
and resulting output.
>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?
In the development version of limma, you can just subset your object.
If RG
is the object produced by read.maimages, then RG[,1] will be an object
with
just the first array, RG[,1:2] will be just the first two arrays,
RG[,-12]
will be all except array 12 etc etc. Similarly, RG[1:100,] will be
just the
first 100 genes. RG[1:100,1] will be the first 100 genes for array 1.
You
can see how it works.
Gordon
>And does anyone have any idea why I am getting the above error??
>
>Thanks in advance for your help :-D
>
>Mick