Displaying 20 results from an estimated 900 matches similar to: "problems saving and loading (PLMset) objects"
2010 Feb 08
1
objects masked from packages
dear all,
I have a problem with a masked object in a package we created here.
we make a package for a workflow of internal analysis of microarray data.
to create the package we used:
> install.packages(pkgs="affyAnalysis", repos=NULL)
> R CMD INSTALL affyAnalysis
Erzeuge Verzeichnisse ...
Erzeuge DESCRIPTION ...
Erzeuge NAMESPACE ...
Erzeuge Read-and-delete-me ...
Kopiere
2012 Jul 24
2
limit of detection (LOD) by logistic regression
Dear all,
I am trying to apply the logistic regression to determine the limit of
detection (LOD) of a molecular biology assay, the polymerase chain reaction
(PCR). The aim of the procedure is to identify the value (variable
"dilution") that determine a 95% probability of success, that is
"positive"/"total"=0.95. The procedure I have implemented seemed to work
looking
2007 Feb 07
2
problems installing R on Linux
Hi everyone,
I am having installation problems, but this is how it all started:
I had some errors running the bioconductor package affyPLM that uses
LAPACK/Blas
> Pset <- fitPLM(Data)
Background correcting PM
Normalizing PM
Fitting models
/usr/local/lib/R/bin/exec/R: relocation error:
/usr/local/lib/R/lib/libRlapack.so: undefined symbol: s_copy
# thrown out of R ....
I was using R
2002 Oct 05
2
R-1.6.0 and R CMD check
Hi,
I upgraded to R-1.6.0 and R CMD check is behaving a bit weird.
The package I am check cannot make it throught because of
errors like
> ##___ Examples ___:
>
> data(Dilution)
> hist(Dilution[,1])
Error in if (log == T) { : missing value where logical needed
Execution halted
while the function called in the example defined in the .Rd fiel
as a signature in which
2012 Oct 04
1
data structure for plsr
I am having a similar problem understanding the data structure of the
"yarn" dataset described in the "[R] data structure for plsr" posts. I have
spectroscopic data I'd like to run through a PLSR and have read the
tutorial series, but still do not understand the data format required for
the code to process my data. My current data structure consists of a .csv
file read into
2005 Apr 11
2
How to calculate the AUC in R
Hello R-listers,
I'm working in an experiment that try to determine the degree of
infection of different clones of a fungus and, one of the measures we
use to determine these degree is the counting of antibodies in the
plasma at different dilutions, in this experiment the maximum number of
dilutions was eleven. I already checked for differences on the maximum
concentration of the
2023 Nov 03
2
'R CMD INSTALL' keeps going on despite serious errors, and returns exit code 0
Hi list,
Here is an example:
??? hpages at XPS15:~$ R CMD INSTALL CoreGx
??? * installing to library ?/home/hpages/R/R-4.4.r85388/site-library?
??? * installing *source* package ?CoreGx? ...
??? ** using staged installation
??? ** R
??? ** data
??? *** moving datasets to lazyload DB
??? ** inst
??? ** byte-compile and prepare package for lazy loading
??? Error : in method for
2006 Feb 21
3
How to get around heteroscedasticity with non-linear leas t squares in R?
Your understanding isn't similar to mine. Mine says robust/resistant
methods are for data with heavy tails, not heteroscedasticity. The common
ways to approach heteroscedasticity are transformation and weighting. The
first is easy and usually quite effective for dose-response data. The
second is not much harder. Both can be done in R with nls().
Andy
From: Quin Wills
>
> I am
2024 Jan 30
2
Use of geometric mean for geochemical concentrations
Dear Rich,
It depends how the data is generated.
Although I am not an expert in ecology, I can explain it based on a biomedical example.
Certain variables are generated geometrically (exponentially), e.g. MIC or Titer.
MIC = Minimum Inhibitory Concentration for bacterial resistance
Titer = dilution which still has an effect, e.g. serially diluting blood samples;
Obviously, diluting the
2009 Jun 06
1
EBImage not loading
Hello all
I've just spent a few joyless hours trying to get EBImage to install in R.
I'm running Ubuntu (Hardy Heron), fully updated (including R and
Imagemagick). EBImage installation seems to work, but when I
'library(EBImage)' I get the following:
- - - -
Error in dyn.load(file, DLLpath = DLLpath, ...) :
unable to load shared library '/home/qilin/R/i486-pc-linux-
2006 Feb 14
2
How to access values returned by R functions (to put into vectors)?
The question is general for all functions, but here is a specific example -
# For the logistic regression of the following correlated variables:
C <- c(457, 1371, 4113, 12339, 37017, 111051, 333153, 999459)
E <- c(0.003858377, 0.014334578, 0.014092836, 0.737950754, 0.996371828,
0.997482379, 1.005569257, 0.994382856)
# The nls function:
A = nls(E~(Em*C^p)/(C50^p + C^p),
2005 Oct 18
2
Installing Bioconductor on R
hi all,
Am new to R. I am having problems installing Bioconductor package in
R on fedora core 4 running on AMD64 bit machine.
this is the error message I get :
gcc -shared -L/usr/local/lib -o affyPLM.so avg_log.o biweight.o
chipbackground.o common_types.o do_PLMrlm.o do_PLMrma.o do_PLMthreestep.o
idealmismatch.o LESN.o lm.o lm_threestep.o log_avg.o matrix_functions.o
2023 Nov 04
1
'R CMD INSTALL' keeps going on despite serious errors, and returns exit code 0
>>>>> Herv? Pag?s
>>>>> on Fri, 3 Nov 2023 15:10:40 -0700 writes:
> Hi list,
> Here is an example:
> ??? hpages at XPS15:~$ R CMD INSTALL CoreGx ??? * installing
> ??? hpages at XPS15:~$ R CMD INSTALL CoreGx
> ??? * installing to library ?/home/hpages/R/R-4.4.r85388/site-library?
2007 Jul 17
2
multiple rugs on a single plot
Hi
I could only find some discussion on this wrt lattice graphics (which I'm
not using). Apologies if I'm missing something obvious.
I'd like to produce 3 rug plots under a kernel density plot for a
population. The population is subdivided into 3 subpopulations, which I'd
like the rug plots to highlight. Naturally, when I do 3 rug plots, they all
plot over each other.
2006 Jan 17
1
Rails too Active?
I feel the need to protest about a disturbing trend in the vibrant RoR
community - name dilution.
ActiveRecord is called that precisely because it is that. The name come
from Martin Fowler, and it expresses a class which is a database record,
only _active_ - that is with methods & behaviors (unlike a classical
database record, which is completely passive.) If you look in the
2009 Dec 26
1
[BioC] How to do RMA without summary to probeset level?
I think that you misunderstood me.
As far as I know, RMA does three things: background correction,
quantile normalization, and summary from probes to probesets. I want
the probe values after background correction and quantile
normalization but before the summary.
On Sat, Dec 26, 2009 at 12:07 PM, Benilton Carvalho <bcarvalh at jhsph.edu> wrote:
> pm(data)
>
> b
>
> On Dec
2006 Mar 23
1
PCA, Source analysis and Unmixing, environmental forensics
I am using R for environmental forensics (determination of the sources
and/or groupings in mixtures of organic chemicals in the field). The
goal is to determine in there are groups of samples with
similar/dissimilar compositions, and to assign samples to a potential
source or a mixture of sources based on the composition (unmixing and
source allocation). Typically there are 10 to 50 chemicals that
2005 Jul 27
1
Installing SJava (I'm almost there, just a little more help please!....please!)
Hi. Day three and Iām still struggling with this. Any advice to overcome the
final hurdle will be enormously appreciated. I now have all the right Java
applications etc. in their right places and have managed to get rid of most
errors but still get this:
ā Making package SJava ā
Building JNI header files...
adding build stamp to DESCRIPTION
running src/Makefile.win
(cd .. ;
2007 Oct 19
1
unable to interactively label curves on a plot
Hello all
Simple question for the gurus. I'm trying to interactively label curves
on a single plot. The labcurve() function from Hmisc seems like the way
to do this (?). I just can't seem to get it to work. Toy example:
> x <- 1:10
> y1 <- x^2
> y2 <- 2*x
> plot(x,y1)
> lines(x,y2)
> labcurve(labels=c("curve1", "curve2"),
2006 Feb 21
2
How to get around heteroscedasticity with non-linear least squares in R?
I am using "nls" to fit dose-response curves but am not sure how to approach
more robust regression in R to get around the problem of the my error
showing increased variance with increasing dose.
My understanding is that "rlm" or "lqs" would not be a good idea here.
'Fairly new to regression work, so apologies if I'm missing something
obvious.