similar to: New package: CHNOSZ

Dear Researches, I am using RF (in regression way) for analize several metrics extract from image. I am tuning RF setting a loop using different range of mtry, tree and nodesize using the lower value of MSE-OOB mtry from 1 to 5 nodesize from1 to 10 tree from 1 to 500 using this paper as refery Palmer, D. S., O'Boyle, N. M., Glen, R. C., & Mitchell, J. B. O. (2007). Random Forest Models

Dear Researches, I am using RF (in regression way) for analize several metrics extract from image. I am tuning RF setting a loop using different range of mtry, tree and nodesize using the lower value of MSE-OOB mtry from 1 to 5 nodesize from1 to 10 tree from 1 to 500 using this paper as refery Palmer, D. S., O'Boyle, N. M., Glen, R. C., & Mitchell, J. B. O. (2007). Random Forest Models

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

... In addition, you may wish to also post on the Bioconductor list for this sort of thing. -- 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 "Bloom County" comic strip ) On Thu, May 3, 2018 at 12:58 AM, Spencer Graves <spencer.graves at effectivedefense.org>

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

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

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

Hi, I have a question about logistic regression in R. Suppose I have a small list of proteins P1, P2, P3 that predict a two-class target T, say cancer/noncancer. Lets further say I know that I can build a simple logistic regression model in R model <- glm(T ~ ., data=d.f(Y), family=binomial) (Y is the dataset of the Proteins). This works fine. T is a factored vector with levels cancer,

/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

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

Hi, I need to upload files larger than 4.4Gb (iso DVD) on CentOS (5.5 x64) http server (httpd-2.2.3-43.el5.centos) On the apache server set in my /etc/php.ini upload_max_filesize = 4900M post_max_size = 5000M In my httpd.conf I set : LimitRequestBody 0 I'm using firefox and/or chrome client for upload a file with 4.2gb size on the server. But it doesn't work.

Dear R-helpers: thank your for your attention. i am a newer to R and i am doing some protein category classification based on the amino acid sequence.while i have some questions urgently. 1. any packages for analysis amino acid sequence 2. given two sequences "AAA" and "BBB",how can i combine them into "AAABBB" 3. based on "AAABBB",how can i get some

?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 >

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

Hi, Is someone has some experience with a nice freeware tool like "DropBox" that I can use on CentOS apache server. I see owncloud, it's a nice tool that I can use with my AD server. Some experience with other freeware tool ? Regards. __________________________ Avant d'imprimer, pensez ? l'environnement ! Please consider the environment before printing ! Ce message et

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

Hi, I installed KVM on a CentOS 7.4 host. The guest is also installed in CentOS 7.4, the network works perfectly. Both Host and Guest machines have the same OS. I do not understand why I have an SSL error on the guest and not on the host while the two computers have the same OS installation. The firewalld, selinux, fail2ban services are not installed on host and guest. Is there an extra

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

Hi, I installed CentOS 5.6 on a Dell Precision Laptop M4600. This laptop has 2 USB 3 connectors. Nothing work (mouse or usb key...) when I connected something on this 2 ports. And sound not working on this laptop. [root at localhost ~]# lspci 00:00.0 Host bridge: Intel Corporation Sandy Bridge DRAM Controller (rev 09) 00:01.0 PCI bridge: Intel Corporation Sandy Bridge PCI Express Root

Dear all, We have developed our own Affymetrix chip (Custom Express Array, PM-only with two species). I want to analyse the data with the limma package, but for that I need to built my own CDF package, probe package and built the filters to analyse one specie or another. I'm using the makeProbePackage available in the AnnotationDbi (for a R-2.13.0) but I got the following error message: