Displaying 20 results from an estimated 100 matches similar to: "Categorical variable in a custom nonlin function with gnm"
2012 Jun 28
1
Merging listed dataset into one
Hello,
I'm wondering how I can merge two featuresets into one.
My dataset is two sets of microarray data and it looks like followings:
> rawData
$v1
TilingFeatureSet (storageMode: lockedEnvironment)
assayData: 2197815 features, 59 samples
element names: channel1, channel2
protocolData
rowNames: LT290677RU_D1_2011-02-16 LT286300LU_D1_2010-07-24 ...
LT003990RU_D1_2010-11-04 (59
2006 Jul 13
1
writeForeignSAS and potential extensions
Dear R-devel,
I've made some potential extensions to writeForeignSAS
in 'foreign' that I wanted to pass along if anyone is
interested. I've attached the diff -u output against
the version found in foreign_0.8-15 and an .R file
with my changes. (In this .R file, the function is named
writeForeignSAS7 to simplify testing/comparisons.)
I've tried to alter the current
2010 Nov 12
0
drosophila2cdf in simpleaffy / affyQCReport
Hi everybody,
I have a problem when trying to do the quality control with the packages
simpleaffy and affyQCReport with the drosophila chip 2.0
At first I got the messeage, that the *.qcdef file is not there. I followed
the instructions in tha manual and created the file like that:
array drosophila2cdf
alpha1 0.05
alpha2 0.065
spk bioB AFFX-r2-Ec-bioB-3_at
spk bioC AFFX-r2-Ec-bioC-3_at
spk bioD
2008 Feb 27
2
problem with creation of eSet
Hi,
I am having troubles with creating an eSet and would appreciate any help on
the following problem.
I am trying to create an eSet using the following code
pd <- read.table(file="pdata.txt",header =TRUE,row.names=1);
colnames(pd) <- c("type","tumor","time","id");
pdN <- list(type =
2008 Mar 20
2
Error in function (classes, fdef, mtable): unable to find an inherited method for function "indexProbes", for signature "exprSet", "character"
Hello Everyone,
I am writing programs in R from 7 months and I am able to solve most of the
errors/issues except for this current post.
My Task is to read a Microsoft Excel file(textE_to_affy.csv) which contains
the Microarray Expression Values collected from the Illumina Microarray
experiment. These collected intensity values need to be normalized(Rank
Invariant Normalization) by using the R
2007 Dec 20
1
custom subset method / handling columns selection as logic in '...' parameter
Dear R-helpers & bioconductor
Sorry for cross-posting, this concerns R-programming stuff applied on
Bioconductor context.
Also sorry for this long message, I try to be complete in my request.
I am trying to write a subset method for a specific class (ExpressionSet
from Bioconductor) allowing selection more flexible than "[" method .
The schema I am thinking for is the following:
2010 Feb 17
0
Help with sigmoidal quasi-poisson regression using glm and gnm functions
Hi everyone,
I'm trying to perform the following regressions in order to compare linear
vs. sigmoidal fit of the relationship between my dependent variable (y) and
one explaining parameter (x2), both including the confounding effects of a
third variable (x1):
quasi-pois-lin <- glm(y ~ x1 + x2, family = quasipoisson(link="identity"),
data=fit)
quasi-pois-sig <- gnm(y ~ x1 +
2012 Apr 02
0
gnm and gnlr3
Hi,
I am quite new to R and would like to do nonlinear regressions with
Poisson distributed data.
I would like to estimate paramters of an equation of this type:
FR = [c*NO * exp(a+b*NO)] / [(c+NO)*(1+exp(a+b*NO))]
a,b and c are parameters, NO are input values
I found both the gnm and gnlr3 function which should be able to do this
regression but I can't manage to make it work.
How can I
2012 Sep 11
1
boot() with glm/gnm on a contingency table
Hi everyone!
In a package I'm developing, I have created a custom function to get
jackknife standard errors for the parameters of a gnm model (which is
essentially the same as a glm model for this issue). I'd like to add
support for bootstrap using package boot, but I couldn't find how to
proceed.
The problem is, my data is a table object. Thus, I don't have one
individual per
2003 Jul 11
2
Nonliner Rgression using Neural Nnetworks
Hi,
I am an old hand at chemistry but a complete beginner at statistics
including R computations.
My question is whether you can carry out nonlinear
multivariate regression analysis in R using neural networks, where the
output variable can range from -Inf to + Inf., unlike discriminant
analysis where the output is confined to one or zero. The library nnet
seems to work only in the latter
2007 Jan 16
1
nonlinear regression: nls, gnls, gnm, other?
Hi all,
I'm trying to fit a nonlinear (logistic-like) regression, and I'd like
to get some recommendations for which package to use.
The expression I want to fit is something like:
y ~ A * exp(X * Beta1) / (1 + exp(-(x + X * Beta2 - xmid)/scal))
Basically, it's a logistic function, but I want to be able to modify
the saturation amplitude by a few parameters (Beta1) and shift the
1997 Dec 19
1
R-beta: Problems porting nlme to R
I have been trying to port the extension 'nlme' ("Classes and methods to fit
and display linear and nonlinear mixed effects models.")to R found on the
Statlib S site. I am having some difficulty. The c code requires at least
S.h and nonlin.h. R has S.h but not nonlin.h. I'm only a recent convert to
R, and have not used S nor SPlus.
Any help is greatly
2012 Apr 27
3
kiteChart to show real values with scalebar
Dear R-users
I hope someone could help me on this problem.
I want to create a multiple kiteChart showing the real values with a
scalebar on each indicating the scale .
Here are some sample data to show what I want to achieve.
Y <- read.table(textConnection("Sample1 Sample2
60 20
150 50
300
2017 Nov 02
0
Cox Regression : Spline Coefficient Interpretation?
Always reply to the list. I do not do private consulting.
(I have cc'ed this to the list).
I still think this belongs on stackexchange, not r-help. I think you need
to read up on the mathematics of spline bases.
Cheers,
Bert
Bert Gunter
"The trouble with having an open mind is that people keep coming along and
sticking things into it."
-- Opus (aka Berkeley Breathed in his
2017 Nov 01
3
Cox Regression : Spline Coefficient Interpretation?
Hi,
I'm using a Cox-Regression to estimate hazard rates on prepayments.
I'm using the "pspline" function to face non-linearity, but I have no clue
how to interpret the result.
Unfortunately I did not find enough information on the "pspline" function
wether in the survival package nor using google..
I got following output:
* library(survival)*
>
>
>
>
2006 Jan 11
3
SPSS and R ? do they like each other?
... and is there also such a nice tool (like spss.get) for exporting
data frames to SPSS? write.table does not keep the data frame labels -
neither did the other exporting tools that I found.
Thanks!
Michael
[[alternative HTML version deleted]]
2010 Mar 03
1
List of zoo dataframes
Hello,
I have various datasets of zoo time series (merged into single frames
via the "merge" command) such as
date var0 var1 var2 var3
08/07/1996 652.54 0.223922 0.515819 0.502638
08/08/1996 662.59 0.997841 0.000383 0.999806
06/09/1996 655.68 0.901685 0.569763 0.866333
08/10/1996 700.64 0.268855 0.244701 0.329285
08/11/1996 730.82 0.438407 0.501427 0.461374
2010 Jul 06
1
nls + quasi-poisson distribution
Hello R-helpers,
I would like to fit a non-linear function to data (Discrete X axis,
over-dispersed Poisson values on the Y axis).
I found the functions gnlr in the gnlm package from Jim Lindsey: this can
handle nonlinear regression equations for the parameters of Poisson and
negative binomial distributions, among others. I also found the function
nls2 in the software package
2008 Nov 25
1
how to check linearity in Cox regression
On examining non-linearity of Cox coefficients with penalized splines - I
have not been able to dig up a completely clear description of the test
performed in R or S-plus.
>From the Therneau and Grambsch book (2000 - page 126) I gather that the test
reported for "linear" has as its null hypothesis that the spline coefficient
is the same at the center of basis. Thus, in the example
1999 Jul 26
1
Logistic regression with coef>0
Hi,
recently I saw but did not pay too much attention to a question
that concerned regression with positive coefficients. In Splus,
thereis the nnls() function that can be used if I am not wrong,
but what about R ?
Now I have the same problem: doing a logistic regression under
constraint that coefs are non negative. What can I do with R?
is there a (weighted) nnls() counterpart available?
Thanks