similar to: Problem with biomaRt::getSequence.

Hi !  Facing problem with " getSequence" commend .  when only biomaRt package loaded the following example working well  >mart <- useMart("ensembl",dataset="hsapiens_gene_ensembl") >seq = getSequence(id="BRCA1", type="hgnc_symbol", seqType="peptide", mart = mart) show(seq) but when i have loaded the seqinr, i got problem

Sometimes the following function call causes a database exception: > gene.seq <- getSequence (id=gene.map[,"ensembl_transcript_id"], type="ensembl_transcript_id", + seqType="3utr", mart=hmart) I understand the above function must be called by try to capture the eventual error. WHat is not clear to me is how to realize that an

Steffen, When the new biomaRt tries to load it errors out because I do not have RMySQL installed. There is not a Windows binary for RMySQL and it does contain C code that I do not know how to build. I do not use the MySQL option in biomaRt. Does RMySQL need to be a required dependency? Below is my screen output and sessionINfo. require(biomaRt) Loading required package: biomaRt Loading required

I executed the following lines several times from a script as well as pasting them in an R shell. Systematically biomaRt is failing. The problem is to extract the 3UTR sequences corresponding to a vector containing 1941 Ensembl Transcript numbers (some are duplicated ... is this s problem ?) Please, find the failing instructions in the following including the ENST vector Any suggestion is

I'm trying to identify the positions of all genes within a specific chromosomal region using biomart. When using the current biomart database I'm able to do this without issue. However, I need to use build 36 of the mouse genome which was last included in ensembl mart 46. I selected this mart and the mouse dataset as follows: mart<-useMart(biomart="ensembl_mart_46",

Hi list, I''ve got an issue at the moment, which isn''t really a big problem, but an untidy annoyance really, and I''d just like to understand what the best practice might be when dealing with the issue. As a really quick summary, the issue is that Puppet is starting up the mysqld service for the first time as unconfined_u, and then when MySQL goes and creates a load

Hi everyone,  I am using bio3d package for some sequence analysis because of its nice integrated MUSCLE execution. However, I have been encountering some errors while I was running seqaln function, which calls for installed MUSCLE program. In my case, I stored the MUSCLE program on the desktop with pathway of "./Desktop/muscle/src/muscle". I had no problem running MUSCLE directly from

Dear R users, There is a error message when I run the following code. It is used to load microarray data and use the top 1000 genes for training svm to classify test set . > library(e1071) Loading required package: class > f=read.table("F:\\lab\\ microarray analysis\\VEH LPS\\exprs.txt",

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

Hi All, I was unable to change location of Dovecot indexes. Currently they are under /var/vmail/%d/%u, but I want to change them to /media/ephemeral0/%u I've changed conf line in /etc/dovecot/dovecot.conf: mail_location = maildir:/var/vmail/%d/%u:INDEX=/media/ephemeral0/%u and setup permissions of /media/ephemeral0 to dovecot:dovecot, tried also vmail:mail (which is default user for

Can biomaRt connect to data base "http://mirecords.umn.edu" or a branch of it ... for instance the validated miRNAs list ..? Thank you very much. Maura tutti i telefonini TIM! [[alternative HTML version deleted]]

I'm using 'getBM' function in Bioconductor package 'biomaRt' to retrieve gene ids based on known chromosome locations. The question is getBM just only return one gene id once a time, even a query is mapped to multiple genes. What's the criteria for picking that special one? [[alternative HTML version deleted]]

-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 On Wed, 11 Jun 2014, igord wrote: > mail_location = maildir:/var/vmail/%d/%u:INDEX=/media/ephemeral0/%u > > and setup permissions of /media/ephemeral0 to dovecot:dovecot, tried also > vmail:mail (which is default user for e-mails) and also tried with 777 on > all dirs, but Dovecot is keeping creating indexes on the old location. I >

-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 On Wed, 11 Jun 2014, igord wrote: >> Did you've restarted Dovecot after changing the conf file? > > Yes, few times. > >> What's in the logs? Maybe you need to enable mail_debug. > > I've enabled now mail_debug, and looks like Dovecot doesn't see new index > location: > > Jun 11 12:36:16 dovecot:

Dear Forum my machine runs Ubuntu 9.04. I am trying to install Biomart, what I realize is that something is missing and it can't install XML, RCurl but I don't know what more to do, I looked in previous posts but I did not find infoprmation that helped. Thanks Andreia biocLite("biomaRt") Running biocinstall version 2.3.14 with R version 2.8.1 Your version of R requires version

I recently updated R 2.10.1 Patched (2010-02-20 r51163) This morning I reinstalled biomaRt using biocLite. Now I can no more connect to biomaRt and even the following instruction is hanging for a while until the same error message pops up. > listMarts() Error in value[[3L]](cond) : Request to BioMart web service failed. Verify if you are still connected to the internet. Alternatively the

I am running the last R version on SuSE 11.1. I installed the Bioconductor environment following the instructions on the web. As a consequence some core packages from Bioconductors were installed. I need to add some more packages. So I tried biomaRt as follows. It does not get installed correctly. Please see the following sequence. Thank you in advance. Maura >

Dear useRs, the seqinR package contains utilities to import and analyze biological sequence data. For a general introduction see this document: http://pbil.univ-lyon1.fr/software/SeqinR//vignette.pdf Please do not use r-help for questions about seqinR or r-bugs for bug report about seqinR. Use instead the seqinR diffusion list: http://pbil.univ-lyon1.fr/software/SeqinR//mailing.php?lang=eng A

Dear useRs, the seqinR package contains utilities to import and analyze biological sequence data. For a general introduction see this document: http://pbil.univ-lyon1.fr/software/SeqinR//vignette.pdf Please do not use r-help for questions about seqinR or r-bugs for bug report about seqinR. Use instead the seqinR diffusion list: http://pbil.univ-lyon1.fr/software/SeqinR//mailing.php?lang=eng A

Dear useR's I have a small basic problem which I am hoping to get some help with. I have a data frame, testSeq_df, with 1 row and 500 columns. Each column is a character (a,c,g or t). I want this sequence to have 4 factors (a,c,g,t). When I try the following: for(i in 1:500){ if (length(levels(testSeq_df[,i]))==1) levels(testSeq_df[,i]) <-