Displaying 20 results from an estimated 2000 matches similar to: "fdrtool qvalues"
2010 Dec 22
0
fdrtool help
Hello,
I am using fdrtool(x, statistic="pvalue") where x is a vector of chisq
p-values.
I can get this command to work with some x, but not with others.
When it does NOT work, I get the following screen output:
> fdrtool(pvals$Chi2.pval, statistic="pvalue")
Step 1... determine cutoff point
Step 2... estimate parameters of null distribution and eta0
Step 3... compute p-values
2010 Jul 16
1
garbage collection & memory leaks in 'R', it seems...
Hello developers,
I noticed that if I am running 'R', type "rm(list=objects())" and
"gc()", 'R' will still be consuming (a lot) more memory than when I then
close 'R' and re-open it. In my ignorance, I'm presuming this is something
in 'R' where it doesn't really do a great job of garbage collection... at
least not nearly as well as
2005 Jun 17
0
Release of new version of caMassClass package and new package caT ools
Hi,
A new version of "caMassClass" package was released today. The package
contain pipeline for processing and classification of protein mass spectra
data.
The main change is off-spinning from the library collection of generic
functions into a new package "caTools". This package, which might be useful
to broader group, is much smaller than "caMassClass" and has fewer
2005 Jun 17
0
Release of new version of caMassClass package and new package caT ools
Hi,
A new version of "caMassClass" package was released today. The package
contain pipeline for processing and classification of protein mass spectra
data.
The main change is off-spinning from the library collection of generic
functions into a new package "caTools". This package, which might be useful
to broader group, is much smaller than "caMassClass" and has fewer
2007 Aug 02
1
sapply?
I have to compare four different grape varieties proteome in two different years. I don't know what test would be more suitable for my data. I think that an anova two way can be usefull also if someone suggested me to perform a manova. In addiction, I can perform each test on a single protein a time, but I can't loose my whole life carrying out anova (I have more than 1000 protein to
2009 Apr 24
0
New package: CHNOSZ
Dear R users,
A new package, CHNOSZ (version 0.8), is available on CRAN.
CHNOSZ is a package for thermodynamic calculations and analysis.
Functions are available for calculating the standard Gibbs energies and
other thermodynamic properties, and chemical affinities, of reactions
between species contained in the thermodynamic database. The database
includes standard thermodynamic properties
2009 Apr 24
0
New package: CHNOSZ
Dear R users,
A new package, CHNOSZ (version 0.8), is available on CRAN.
CHNOSZ is a package for thermodynamic calculations and analysis.
Functions are available for calculating the standard Gibbs energies and
other thermodynamic properties, and chemical affinities, of reactions
between species contained in the thermodynamic database. The database
includes standard thermodynamic properties
2004 May 17
0
Bioconductor 1.4 released
Greetings!
The Bioconductor core group would like to announce the 5th release of
Bioconductor, version 1.4. There are many new packages as well as
several major upgrades and fixes in older packages, and users are
encouraged to upgrade existing tools and check out the new packages.
Release 1.4 is intended to be operated with R version 1.9.x, which can
be obtained at CRAN
2012 Oct 30
1
Is there an lm() equivalent of panel.lmline()?
panel.lmline returns intercept and slope of y ~ x subsetted to the
combination of conditioning factors given to xyplot in lattice.
for instance:
xyplot(Xvalues ~ log(Qvalues)|Tfac, data = df7, panel = panel.lmline)
I am looking to find the equivalent formulation for lm() proper. If I do
this:
lmcal <- lm(Xvalues ~ log(Qvalues):Tfac, data = df7)
Only one value of the intercept is returned.
2011 Mar 22
2
Data frame and function that requires vector as input
Hi,
I have a data.frame(zscores) that looks like this:
gA gB
g1 0.2 0.6
g2 0.3 Na
My problem is that I need to use a function and the output is a vector
of only the non NA values, so shorter than the list I would obtain
dropping the data.frame.
What is the cleanest way to keep row and column names or putting the
values back into the same data frame format?
The function
2008 Feb 20
1
R square for Monotone regression
I'm using the monoreg function (with weights) from the fdrtool package.
How can I calculate the R square for this type of regression?
Thanks for your help,
Thierry
--
View this message in context: http://www.nabble.com/R-square-for-Monotone-regression-tp15580803p15580803.html
Sent from the R help mailing list archive at Nabble.com.
2013 Jan 09
0
[solved] t-test behavior given that the null hypothesis is true
Hi Ted,
yes this was the problem. Thank you very much.
best
idaios
On Wed, Jan 9, 2013 at 4:51 PM, Ted Harding <Ted.Harding@wlandres.net>wrote:
> Ah! You have aqssigned a parameter "equal.var=TRUE", and "equal.var"
> is not a listed paramater for t.test() -- see ?t.test :
>
> t.test(x, y = NULL,
> alternative = c("two.sided",
2013 May 16
2
R looping help
Hey I'm not really sure what I should put on here, but I am having trouble
with my R code. I am trying to get the p-values, R^2s etc for a number of
different groups of variables that are all in one dataset.
This is the code:
#Stand counter
st<-1
#Collections
stands<-numeric(67)
slopes<-numeric(67)
intercepts<-numeric(67)
mses<-numeric(67)
rsquares<-numeric(67)
2007 Jun 29
1
Shapiro Test P Value Incorrect? (PR#9768)
Full_Name: Jason Polak
Version: R version 2.5.0 (2007-04-23)
OS: Xubuntu 7.04
Submission from: (NULL) (137.122.144.35)
Dear R group,
I have noticed a strange anomaly with the shapiro.test() function. Unfortunately
I do not know how to calculate the shapiro test P values manually so I don't
know if this is an actual bug.
So, to produce the results, run the following code:
pvalues = 0;
for
2006 Jul 31
0
Three questions about a model for possibly periodic data with varying amplitude
Hi dear R community,
I have up to 12 measures of a protein for each of 6 patients, taken
every two or three days. The pattern of the protein looks periodic,
but the height of the peaks is highly variable. It's something like
this:
patient <- data.frame(
day = c(1, 3, 5, 8, 10, 12, 15, 17, 19, 22, 24, 26),
protein = c(5, 3, 10, 7, 2, 8, 25, 12, 7, 20, 10, 5)
)
plot(patient$day,
2010 May 11
1
comparing and combing files
Hello,
I have two tab-delimited files which I would like to combine.
In the first one I have gene IDs (Unique) on column 1 and than various
experimental results from microarray analysis (see attached files list1 )
the second arrays have the same genes IDs (more and in a different order,
some are double) (see attached files list2 )
What I would like to do is to search in the second list for gene
2011 Apr 07
1
Two questions about metacharacter in regexprs and function return
for the script, please kindly see the script below. At line 10 and line 13,
my problems occurs.
The first one is I try to retrieve the gene official name from a column of a
table. The pattern of official name is something starting with gene_name.
For detail problems, please see the according lines.
Any suggestions are appreciated
example of matching source (extract the Nnat, sometime it would
2007 May 23
2
problem with read.table
Dear all,
I try to use read.table to get the data from a tab delimited file, and some
of the data is shown below:
3185 heterogeneous nuclear ribonucleoprotein F
3187 heterogeneous nuclear ribonucleoprotein H1 (H)
3188 heterogeneous nuclear ribonucleoprotein H2 (H')
3189 heterogeneous nuclear ribonucleoprotein H3 (2H9)
3190 heterogeneous nuclear ribonucleoprotein K ///
2012 Aug 10
3
Parsing large XML documents in R - how to optimize the speed?
Hello everyone,
I would like to parse very large xml files from MS/MS experiments and
create R objects from their content. (By very large, I mean going up to
5-10Gb, although I am using a 'small' 40M file to test my code.)
My first attempt at parsing the 40M file, using the XML package, took more
than 2200 seconds and left me quite disappointed.
I managed to cut that down to around 40
2010 May 18
1
GUI commands to call for a protein from protein data bank
What I am trying to do is use GUI function, traitr, and to call for a pdb
file and save it and then display it. I want to call for it by taking it
from the user and then displaying it on the screen. I am having problems
with that. The line pdb <- read.pdb(""ProteinCode) where proteincode should
be the name of the protein, for example 1ly2, but it always ends up being
protein. My