Displaying 20 results from an estimated 1400 matches similar to: "predict.glm -> which class does it predict?"
2009 Aug 21
1
LASSO: glmpath and cv.glmpath
Hi,
perhaps you can help me to find out, how to find the best Lambda in a
LASSO-model.
I have a feature selection problem with 150 proteins potentially
predicting Cancer or Noncancer. With a lasso model
fit.glm <- glmpath(x=as.matrix(X), y=target, family="binomial")
(target is 0, 1 <- Cancer non cancer, X the proteins, numerical in
expression), I get following path (PICTURE
2009 Sep 18
1
lapply - value changes as parameters to function?
Hi,
I'm trying to get better at things like lapply but it still stumps
me. I have a function I've written, tested and debugged using
individual calls to the function, ala:
ResultList5 = DoAvgCalcs(IndexData, Lookback=5,
SampleSize=TestSamples , Iterations=TestIterations )
ResultList8 = DoAvgCalcs(IndexData, Lookback=8,
SampleSize=TestSamples , Iterations=TestIterations )
ResultList13
2005 Jun 02
3
trouble getting speex_echo_cancel() to work
> - set sampling rate to 8 kHz (at least for now)
> - make sure the far end signal in the playback signal is always a bit in
> advance (never late) compared to the mic signal.
> - Set the tail length to something around 100 ms.
>
> Also, if you're using two different soundcards (as I understand) for the
> playback and the capture, you're *never* going to get echo
2006 Mar 26
1
Newbie clustering/classification question
My laboratory is measuring the abundance of various proteins in the
blood from either healthy individuals or from individuals with various
diseases. I would like to determine which proteins, if any, have
significantly different abundances between the healthy and diseased
individuals. Currently, one of my colleagues is performing an ANOVA on
each protein with MS Excel. I would like to analyze
2024 Apr 16
5
read.csv
Dear R-developers,
I came to a somewhat unexpected behaviour of read.csv() which is trivial but worthwhile to note -- my data involves a protein named "1433E" but to save space I drop the quote so it becomes,
Gene,SNP,prot,log10p
YWHAE,13:62129097_C_T,1433E,7.35
YWHAE,4:72617557_T_TA,1433E,7.73
Both read.cv() and readr::read_csv() consider prot(ein) name as (possibly confused by
2012 Mar 02
2
Statistical Histograms in R
Hi,
I'm wondering if anybody could possibly help me?
I have a table with 5 tab-delimited columns. Each column has 'e-value'
scores for 5 different proteins.
I'd like to plot a distribution curve using hist() for the 5 different
proteins and show the 5 distribution curves on the same graph in different
colours.
In the case, E-values will be the X-axis and frequency will be the
2024 Apr 16
1
read.csv
?s 11:46 de 16/04/2024, jing hua zhao escreveu:
> Dear R-developers,
>
> I came to a somewhat unexpected behaviour of read.csv() which is trivial but worthwhile to note -- my data involves a protein named "1433E" but to save space I drop the quote so it becomes,
>
> Gene,SNP,prot,log10p
> YWHAE,13:62129097_C_T,1433E,7.35
> YWHAE,4:72617557_T_TA,1433E,7.73
>
2009 Sep 16
1
expression
/Dear all,///
/I am very thankful, if you could tell what is the right way to write:
mtext(paste(expression("R"^2),round(marco2[1,i],digits=3)," N? of proteins:",marco3[i]),side=4,cex=.6)
in this case the output is:
"R"^2
I tried also in this way:
mtext(paste(expression(paste("R"^2)),round(marco2[1,i],digits=3)," N? of
2024 Apr 16
1
read.csv
Gene names being misinterpreted by spreadsheet software (read.csv is
no different) is a classic issue in bioinformatics. It seems like
every practitioner ends up encountering this issue in due time. E.g.
https://pubmed.ncbi.nlm.nih.gov/15214961/
https://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-1044-7
https://www.nature.com/articles/d41586-021-02211-4
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
2009 Apr 17
5
Binomial simulation
Hi Guy's
I was wondering if someone could point me in the right direction.
dbinom(10,1,0.25)
I am using dbinom(10,1,0.25) to calculate the probabilty of 10 judges
choosing a certain brand x times.
I was wondering how I would go about simulating 1000 trials of each x value
?
regards
Brendan
--
View this message in context:
2012 Jul 23
3
How to do the same thing for all levels of a column?
Dear all,
I am a R beginner, and I am looking for a way to do the same thing for all
levels of a column in a table.
Basically, I have a bunch of protein sequences composed of different amino
acid residues, and each residue is represented by an uppercase letter. I
want to calculate the ratio of different amino acid residues at each
position of the proteins. Here is an example table:
Proteins
2018 May 03
3
Package for Molecular Properties
All
Is there a package or library that will, given a nucleotide sequence
1. calculate the extinction coefficient at 260 nm for (Beer-Lambert's law)
2. calculate molecular weight
3. return it's complementary sequence
I was able to find several packages that can do similar calculations for an amino acid sequence for proteins but none for nucleic acids.
Any pointers, etc. would be
2012 Mar 08
4
Correlation between 2 matrices but with subset of variables
Dear All,
I have two matrices A (40 x 732) and B (40 x 1230) and would like to calculate correlation between them. I can use: cor(A,B, method="pearson") to calculate correlation between all possible pairs. But the issue is that there is one-many specific mappings between A and B and I just need to calculate correlations for those pairs (not all). Some variables in A (proteins, say p1)
2009 Jul 14
2
hi friends, is there any wait function in R
hi,
is there any wait function in R. I am running one R script to plot
many graphs it is in the for loop. its showing no error but its not
plotting well I think i can solve this problem with a wait function.
Please help me in this regards. If u need any clarification about
programme. u can find the script below.
best regards,
Deepak.M.R
Biocomputing Group
University of Bologana.
#!/usr/bin/R
2010 Aug 17
1
ROCR predictions
Hi everybody,
I am having a problem building a ROC curve with my data using the ROCR
package.
I have 10 lists of proteins such as attached (proteinlist.xls). each of the
lists was calculated with a different p-value.
The goal is to find the optimal p-value for the highest number of true
positives as well as lowaest number of false positives.
As far as I understood the explanations from the
2010 Dec 10
2
survival package - calculating probability to survive a given time
Dear R users,
i try to calculate the probabilty to survive a given time by using the
estimated survival curve by kaplan meier.
What is the right way to do that? as far as is see i cannot use the
predict-methods from the survival package?
library(survival)
set.seed(1)
time <- cumsum(rexp(1000)/10)
status <- rbinom(1000, 1, 0.5)
## kaplan meier estimates
fit <- survfit(Surv(time,
2010 May 20
2
Overlap of leaf labels
Hi,
I have tried looking at the archives but havent found any answer that works
till now (Sorry if i have missed anything)
I am a newbie to R and i am trying to carry out hierarchical clustering
using hclust -> as.dendrogram and then plotting the results as a dendrogram
using the plot function plot(object).
My question is :
In the function "plot", can one decrease the leaf label
2018 May 03
0
Package for Molecular Properties
library(sos)
(mp <- findFn('{molecular properties}'))
????? ** found 7 matches in 4 packages and opened two web pages in my
default browser with (a) the 7 matches and (b) the 4 packages. The first
function was something for amino acids, like you suggested.? Two others
returned compound and substance information from PubChem.
????? Does this help?
????? Spencer
On
2005 Jan 16
2
Empirical cumulative distribution with censored data
Dear list,
I would like to plot the empirical cumulative distribution of the time
needed by a treatment to attain a certain goal. A number of
experiments is run with a strict time limit. In some experiments the
goal is attained before the time limit, in other experiments time
expires before the goal is attained. The situation is very similar to
survivial analysis with censored data. I tryed