[R] loess plot

[Bert Gunter]

1. Please don't double post.

2. You probably have some "synthesized" values that are 0 and so get -Inf
for their logs, which is NaN, thereby producing the error messages.

Failing that, your data may be messed up in some way (character values,
stray non-characters, ...)

-- Bert Gunter 

-----Original Message-----
From: r-help-bounces at r-project.org [mailto:r-help-bounces at r-project.org] On
Behalf Of shetumi at aim.com
Sent: Friday, May 30, 2008 7:32 AM
To: r-help at r-project.org
Subject: [R] loess plot

I was trying to plot some data in R. I used the following code to draw a
loess fit and got the output as

>?lines(lowess(log(abs(t(res))), log(abs(t(synthesised)))), col="red")
Error in lowess(log(abs(t(res))), log(abs(t(synthesised)))) :?? NA/NaN/Inf
in foreign function call (arg 1)
Then I thought to use your Limma package for background correction. Do you
think it's a right choice ? 

However, I installed Limma using
> source("http://www.bioconductor.org/biocLite.R")
> biocLite("limma")
> biocLite("statmod")
> library(limma)

and then used the commands which generated the error as follows --

> system.time(fit <- loessFit( log(abs(t(res))), log(abs(t(synthesised)))))
Error in loessFit(log(abs(t(res))), log(abs(t(synthesised)))) : 
? binary operation on non-conformable arrays
Timing stopped at: 0.57 0.06 0.64 NA NA 

> system.time(fit <- plotPrintTipLoess( log(abs(t(res))),
log(abs(t(synthesised)))))
Error in 1:layout$ngrid.c : NA/NaN argument
In addition: Warning messages:
1: In object$printer :
? $ operator is invalid for atomic vectors, returning NULL
2: In object$M : $ operator is invalid for atomic vectors, returning NULL
3: In object$A : $ operator is invalid for atomic vectors, returning NULL
4: In object$M : $ operator is invalid for atomic vectors, returning NULL
5: In object$A : $ operator is invalid for atomic vectors, returning NULL
6: In layout$ngrid.c :
? $ operator is invalid for atomic vectors, returning NULL
Timing stopped at: 0.66 0.01 0.67 NA NA 


Can someone please?tell me where the problem is and?what could be the
right?command to use ? 



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