similar to: Non-parametric (M)ANOVA with R ?

Hi, I'm trying to calculate p-value to findout definitely expressed genes compare A to B situation. I got this data(this is a part of data) from whole organism , and each number means each expression values (that means, we could think 'a' gene is 13 in A situation, and it turns 30 in B situation) To findout probability, I'm going to use Audic - Claverie Method. ( The significance

Hi: I am trying to query pubmed abstracts using the following syntax: url= "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?" search = paste(url, "db=pubmed&term=", queryTerm1, "+AND+", queryTerm2,"+OR+",queryTerm3, "+OR+", queryTerm4, "[abstract]&retmax=100&usehistory=y", sep="") docId <-

Dear R folks: I am trying to use SSOAP (version 0.2-2) package in R (version 2.1.0,linux) to access SOAP service on NCBI (http://www.ncbi.nlm.nih.gov) its WSDL file is at http://www.ncbi.nlm.nih.gov/entrez/eutils/soap/eutils.wsdl but some errors occured: > ncbi <- processWSDL("http://www.ncbi.nlm.nih.gov/entrez/eutils/soap/eutils.wsdl") > ff <-

Hi dear Rers, I am using SSOAP package to access SOAP service at NCBI. I followed the example code in SSOAP but failed. > z <- .SOAP("http://www.ncbi.nlm.nih.gov/entrez/eutils/soap/soap_adapter.cgi", method="run_eInfo", db="pubmed", action = I("einfo")) Error: protect(): protection stack overflow what's wrong? Thanks very much. Regards

Hi: I am trying to search PubMed abstracts which contains BOTH two terms: COL4A1 AND Ocular. I am using the following code: url= "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?" search = paste(url, "db=pubmed&term=COL4A1+AND+Ocular[abstract]&retmax=300", sep="") docId <- xmlTreeParse(getURL(paste(url, search, sep="")),

I''d like to extend bleucloth or redcloth to support custom tags, e.g. I want to use markup like this: [pubmed:18332676] which shall be extended to: <a href="http://www.ncbi.nlm.nih.gov/pubmed/18332676">Behav Pharmacol. 2008 Mar;19(2):121-128.</a> Does anyone know, if this is possible and has some hints how to do this?! I have not decided, wether I want to use

I would like to track in which journals articles about a particular disease are being published. Creating a pubmed search is trivial. The search provides data but obviously not as an R dataframe. I can get the search to export the data as an xml feed and the xml package seems to be able to read it. xmlTreeParse("

I want to analyze binary, multinomial, and count outcomes (as well as the occasional continuous one) for clustered data. The more I search the less I know, and so I'm hoping the list can provide me some guidance about which of the many alternatives to choose. The nlme package seemed the obvious place to start. However, it seems to be using specifications from nls, which does non-linear

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, After searching the archives and Google and not turning up anything, I thought I'd ask here. Has anyone done an R package for calculating Gwet's AC1 statistic and variance? K.L. Gwet. Computing inter-rater reliability and its variance in the presence of high agreement. Br J Math Stat Psychol. 2008 May;61(Pt 1):29-48. http://www.ncbi.nlm.nih.gov/pubmed/18482474 Thanks, --pete

Hello, Have anybody made tools for g-estimation (introduced by J. Robins) in R. http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=ShowDetailView&TermToSearch=8235180&ordinalpos=3&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum Regards, Jari Haukka

Hi R users,I am a beginner in the use of R. I need urgent help for my thesis study. <https://stats.stackexchange.com/posts/633206/timeline> I have daily air pollution parameters PM10, PM2.5 CO, NO2, SO2, and O3. I also have daily hospital admission numbers. Taking into account the effect of weekends and holidays, I would like to used generalised additive model (GAM) to explore the

Hello Arno, FreeNAS doesn't come with a compiler and I had to compile with the patch on FreebBSD-9.3 and then copy the produced mge-shut. Unfortunately it didn't work out. For every try I was getting "Connection Refused" and when I tried /usr/local/libexec/nut/mge-shut -D -a <ups_name> I was always getting 'No matching HID UPS found'. I returned back to the

A summary of my problem, I had wrong UIDs for a user (eg pmal) between the /etc/passwd file and the smbpasswd file. When I was trying to loggin from a couple of machines running either win nt or win 98 I was reading in the log files that the loggin could not be completed because the UID were wrong but there were instances were I could loggin from another computer with the same username. I really

Hi Panagiotis 2015-04-06 9:13 GMT+02:00 Panagiotis Kritikakos < panagiotis.kritikakos at nikitec.gr>: > Hello Arno, > > Can apply the patch directly or should I recompile nut? > not sure to fully understand your comment, but... this is a source code patch, so you indeed have to apply it to the NUT source code (from within the source tree, "patch -p1 <

Hello Arno, Thanks for the quick reply. FreeNAS is FreeBSD-based. Yes, I could test a patch. As I have mentioned, this behavior is not seen at every single reboot but after most reboots. Also, some times, the connectivity can be lost without even rebooting. That is not very often can have happened a few times. Best regards, Panagiotis On 2/4/2015 5:44 ??, Arnaud Quette wrote: > Hello

Hi, I actually need to download pdfs through R code. The thing which I want to do is that, search for a paper in pubmed, which is possible by using GetPubMed function in the package "NCBI2R?". GetPubMed(searchterm, file = "", download = TRUE , showurl = FALSE, xldiv = ";", hyper = "HYPERLINK", MaxRet = 30000, sme = FALSE, smt = FALSE, quiet = TRUE,

Hello Arno, Can apply the patch directly or should I recompile nut? Best regards, Panagiotis On 3/4/2015 5:06 ??, Arnaud Quette wrote: > Hello Panagiotis > > 2015-04-03 14:28 GMT+02:00 Panagiotis Kritikakos > <panagiotis.kritikakos at nikitec.gr > <mailto:panagiotis.kritikakos at nikitec.gr>>: > > Hello Arno, > > Question: have you also

Hello! I am crossposting this to R-help and BioC, since it is relevant to both groups. I wrote a wrapper for Entrez search utility (link for this is provided bellow), which can add some new search functionality to existing code in Bioconductor's package 'annotate'*. http://eutils.ncbi.nlm.nih.gov/entrez/query/static/esearch_help.html Entrez search utuility returns a XML document

I'm trying to read some web tables directly into R. These are both genome sequencing projects (eukaryotes and metagenomes) from NCBI and look very similar; however, only the first one works. http://www.ncbi.nlm.nih.gov/genomes/leuks.cgi http://www.ncbi.nlm.nih.gov/genomes/lenvs.cgi I added ?dump=selected to the end of the url string to get a tab- delimited file (which is what happens