search for: rna

Again I would like to express my deepest appreciation to all those working so selflessly on the development of R for us all to use it freely (and it is such a joy to use!) Rashid Nassar == Possible bug: 1. boxplot() This is an old behavior that I had reported before, but as it is still there, it may not ba a bug (although it looks like one to me). "qfcut" is numeric, "st"

A couple of help page typos that I came across: 1. help(sample) Arguments: x: Either a (numeric, complex, character or logical) vector of more than one elements from which to choose, or a positive ^ [element] 2. help(delay) Description: `delay' creates a promise to evaluate the given expression in the

...e-sized (to make it larger). I am constructing an 8x12 matrix of scatterplots each containing approx 600 points. In order to get them in the window I remove the axes etc., quartz() par(mfrow=c(8,12), mar=c(0,0,0,0), oma=c(0,0,0,0)) for(i in 1:8){ # Row counter for(j in 1:12){ # Col counter plot(rna$red[(rna$row==levels(rna$row[i])&(rna$col==j)], rna$tof[(rna$row==levels(rna$row[i])&(rna$col==j)], xlab="tof",ylab="green",xaxt="n",yaxt="n", ann=FALSE,xlim=c(0,100),ylim=c(0,300),pch=".") } } Here is the problem: how many...

...ng HA with round robin) the Mail.app client got to one dovecot repository on one tcp connection and then on the other. Is there a reason why syncing tis move from new to cur is a bad idea? Gerben Wierda (LinkedIn <https://www.linkedin.com/in/gerbenwierda>) R&A IT Strategy <https://ea.rna.nl/> (main site) Book: Chess and the Art of Enterprise?Architecture <https://ea.rna.nl/the-book/> Book: Mastering ArchiMate <https://ea.rna.nl/the-book-edition-iii/> > On 17 Jan 2023, at 22:41, Gerben Wierda <gerben.wierda at rna.nl> wrote: > > I can confirm this in...

Hi all, new to this forum I'm try to using R to draw a heatmap of my RNA-seq data before doing that I did a log2 transformation of my data and produce a lot -inf in the matrix when I try to use the heatmap function, it seems can not deal with the -inf so I was wondering how to deal with these gene with 0rpkm(they are not 0 in all samples, so I want to keep them in the...

On January 6, 2023 3:56:39 AM GMT+02:00, Gerben Wierda <gerben.wierda at rna.nl> wrote: >One step further in my quest to create a replacement mail server. > >I now have my old mail server (2.3.19.1, macOS + MacPorts) and my new (2.3.20, Alpine Linux, Docker, apk package). When I turn on replication it works, but, after a while I see: > >Jan 06 00:50:31 rep...

I am finding on all my CentOS 5.8 systems (all fully updated but a variety of package mixes) that the display or convert commands from ImageMagick are unable to handle eps files. I get error output as follows, curious if anyone else sees this $ convert rna.eps rna.epi convert rna.eps rna.epi Error: /undefinedfilename in (72x72) Operand stack: Execution stack: %interp_exit .runexec2 --nostringval-- --nostringval-- --nostringval-- 2 %stopped_push --nostringval-- --nostringval-- --nostringval-- false 1 %stopped_push Dictionar...

...in a slightly different setting, but still using two-way sync between two dovecots. On e is 2.3.19.1 running on macOS Monterey, the other is 2.3.20 running in an alpine container on Ubuntu. Gerben Wierda (LinkedIn <https://www.linkedin.com/in/gerbenwierda>) R&A IT Strategy <https://ea.rna.nl/> (main site) Book: Chess and the Art of Enterprise?Architecture <https://ea.rna.nl/the-book/> Book: Mastering ArchiMate <https://ea.rna.nl/the-book-edition-iii/> > On 15 Jan 2023, at 23:12, Tomaz Kavcic <tomaz.kavcic at futurion.si> wrote: > > Hello, > > I...

...ar All, I'me having (much) trouble understanding why it happened and answering a referee's comment to part of a submitted manuscript. I've tried to google for help but... I'm really confident that although this is a R-Help list someone can help me! I used R to do an ANCOVA w/ RNA/DNA as the dep var, sl as the indep var and gut (a factor w/ levels: prey and empty) as the covariate: > RNADNA.sl.gut<-lm(sqrt(RNADNA)~gut*sl,subset=gut!="Yolk-sac",data=cond) > summary(RNADNA.sl.gut) The results from this are: (...) Coefficients: Estimate Std...

Dear All, When I plot the values and linear regression line for one data set, it is fine. But for another one I see zigzags, when I plot the confidence interval >cd Depth CHAOsep12RNA 9,94 804 25,06 1476,833333 40,04 1540,561404 50,11 1575,166667 52,46 349,222222 54,92 1941,5 57,29 1053,507042 60,11 1535,1 70,04 2244,963303 79,97 1954,507042 100,31 2679,140625 > plot(cd$CHAOsep12RNA,cd$Depth, ylim = rev(range(0:100)), xlab="CHAO", ylab="Depth", pch=15, l...

2014-02-25 10:12 GMT+01:00 Virgo P?rna <virgo.parna at mail.ee>: > On Sun, 23 Feb 2014 19:39:02 +0100, Josu Lazkano <josu.lazkano at gmail.com> wrote: >> >> # dmesg >> ... >> [181041.636190] usb 4-4: new low-speed USB device number 2 using ohci_hcd >> > > I recently read about openw...

...st will suit an applicant from a strong computational background who wishes to apply their knowledge to help develop a better understanding of the processes that control how tumours develop. Details below:- High Performance Computing applied to cancer research: Computational analysis of Noncoding RNA regulators of gene expression in individual tumour cells RNABiology/Computational Biology The goal of this project is to use computational tools to ask how patterns in gene expression are disrupted in cancer. The project will suit a graduate student from a computational background with exceptional...

...e "question" was not related to - the use of - R). Now I think I can soundly make my point w/ the referee (can I use your replies? If so I intend to properly cite its use?!?). Regards, Eduardo Esteves ps - Sorry for not explaining the "biological details" of my posting: RNA/DNA is the ratio of RNA content to DNA content obtained for individual fish larvae (plus for each one I noted if it had visible prey items in the gut or not, thus the levels Prey and Empty of factor Gut); and sl is the standard length (distance from the tip of snout to the posterior extremi...

...rning: replication(sysbh): Remote sent invalid input: - I've removed synchronous operation for now (found a message on the net suggesting that) but is this known and what does it mean? Gerben Wierda (LinkedIn <https://www.linkedin.com/in/gerbenwierda>) R&A IT Strategy <https://ea.rna.nl/> (main site) Book: Chess and the Art of Enterprise?Architecture <https://ea.rna.nl/the-book/> Book: Mastering ArchiMate <https://ea.rna.nl/the-book-edition-iii/> -------------- next part -------------- An HTML attachment was scrubbed... URL: <https://dovecot.org/pipermail/dov...

...cot/cert/mail.hamletdevelopments.ca > } > > pg sql support supporting replication > > # cat dovecot-pgsql.conf > driver = pgsql > connect = host=localhost port=5433 dbname=scom_billing user=pgsql password= > default_pass_scheme = PLAIN > > password_query = SELECT username as user, password FROM email_users WHERE username = '%u' and password <> 'alias' and status = True and destination = '%u' > > user_query = SELECT home, uid, gid FROM email_users WHERE username = '%u' and password <> 'alias' and status = T...

Hi, R-help, I have a group of data from RNA-seq want to be analyzed by Fisher's exact test in R. I want to compare the significant difference of about 30,0000 individuals in two different samples, and I have no idea how to use R, so could you please give me some suggestions or the scripts for Fisher's exact test? Thank you very muc...

Hi all , I have one query. i have list of some .cel files. in my program i have to mention the path of these .cel files part of my program is, rna.data<-exprs(justRMA(filenames=file.names, celfile.path=*datadir*, sampleNames=sample.names, phenoData=pheno.data, cdfname=cleancdfname(hg18_Affymetrix U133A))) in the place of "datadir" i have to mention the character string of the directory of these .cel files. I don't know how...

Dear all, I wrote the following batch script on a iMac, and ran it on a linux mosix cluster. tu <- read.table("cage.mm5.tags.rna_lib.CAA-CAJ.tu-reshape.table") tu_reshaped <- t(reshape(tu[1:50,], direction="wide", timevar="tu", idvar=c("rna","lib"))) write.table(tu_reshaped, "cage.mm5.tags.rna_lib.CAA-CAJ.tu-reshaped.table") q(sav="no") (I will remove the [...

...>> >> pg sql support supporting replication >> >> # cat dovecot-pgsql.conf >> driver = pgsql >> connect = host=localhost port=5433 dbname=scom_billing user=pgsql >> password= >> default_pass_scheme = PLAIN >> >> password_query = SELECT username as user, password FROM email_users >> WHERE username = '%u' and password <> 'alias' and status = True and >> destination = '%u' >> >> user_query = SELECT home, uid, gid FROM email_users WHERE username = >> '%u' and password &l...

I have a very basic question about limma. Assume I have experiments from 3 or more RNA sources in a reference design. It is easy to define individual contrasts but I want to specify a contrast matrix that tests for significant differences among ALL the different RNA sources (i.e. the analogous thing to a simple One-Way ANOVA). How can I do that? Thanks! Max --