User: Steffen Durinck

gravatar for Steffen Durinck
Reputation:
420
Status:
Trusted
Location:
Last seen:
13 years ago
Joined:
15 years, 6 months ago
Email:
s*******@ebi.ac.uk

Posts by Steffen Durinck

<prev • 42 results • page 1 of 5 • next >
0
votes
2
answers
378
views
2
answers
Answer: A: biomaRt: how to find RCurl package ?
... Hi, The RCurl package is part of the omegahat project. You can find the package here: http://www.omegahat.org/RCurl/ best, Steffen > Hello list members > > package biomaRt requires RCurl package, > but I didn't manage to find it anywhere... > It is not existing in package listing ...
written 13.0 years ago by Steffen Durinck420
0
votes
1
answer
637
views
1
answers
Comment: C: biomaRt error
... Hi, > My understanding is that the BioMart folks are making changes to the > table names for the BioMart database, and this is happening right now > (e.g, right after BioC 1.8 is released). Unfortunately this means that > some of the convenience functions like getGene() are being broken ...
written 13.1 years ago by Steffen Durinck420
0
votes
1
answer
491
views
1
answers
Comment: C: biomaRt and ensembl tables
... Dear Tabare, biomaRt tries to contain as minimal as possible hard coded information on the BioMart databases and as such to be robust to new BioMart database releases. The getBM function contains no hard-coded information on the databases and should always work. The 'simpler' biomaRt functions su ...
written 13.1 years ago by Steffen Durinck420
0
votes
1
answer
505
views
1
answers
Answer: A: Gene-GO
... Hi, You'll find more infomation on GO annotations here: http://www.ebi.ac.uk/GOA/ For human check out: http://www.ebi.ac.uk/GOA/HUMAN_release.html best, Steffen > > Can somebody please provide info. on the total number of genes in the > human > genome that have been annotated to GO ...
written 13.1 years ago by Steffen Durinck420
0
votes
2
answers
770
views
2
answers
Answer: A: Help with annotation packages
... Hi Amy, > My confusion is really over which package to use: > > I understand that Biomart can handle single queries or queries for a small > list of (e.g.) DE genes, but not the entire probe set. Is that right? This is not true. You can use it for long lists as well, the maximum I t ...
written 13.2 years ago by Steffen Durinck420
0
votes
1
answer
622
views
1
answers
Answer: A: Biomart useDataset error
... Hi Aedin, You should upgrade biomaRt and use the latest version (1.5.10, see developmental packages). Best, Steffen > Dear BioC and Steffen > I'd be grateful for your help. I getting an xmlTreeParse error with > useDataset() > Thanks > Aedin > > > listDatasets(mart) > ...
written 13.2 years ago by Steffen Durinck420
0
votes
5
answers
753
views
5
answers
Comment: C: Quick start to linking GO terms and microarray data
... Hi Mick, The biomaRt package can retrieve data from BioMart data management systems (see: http://www.biomart.org). Any database that provides such a BioMart implementation can thus be queried. Ensembl and Wormbase for example provide this and are queried in real-time through biomaRt. For species ...
written 13.2 years ago by Steffen Durinck420
0
votes
5
answers
753
views
5
answers
Comment: C: Quick start to linking GO terms and microarray data
... Hi, Next to Ensembl, biomaRt currently includes Wormbase, VEGA, Uniprot and msd. Soon I expect plants to be represented as well via the Gramene database (http://www.gramene.org). Best, Steffen michael watson (IAH-C) wrote: >Hi Steffen, Wolfgang > >Thanks a lot, the biomaRt package look ...
written 13.2 years ago by Steffen Durinck420
0
votes
5
answers
753
views
5
answers
Comment: C: Quick start to linking GO terms and microarray data
... Hi Mike, As Wolfgang already suggested you can do this with the biomaRt package. Here is how should do this: > library(biomaRt) Loading required package: XML Loading required package: RCurl > mart = useMart("ensembl",dataset="hsapiens_gene_ensembl") Checking attributes and filters ... ok ...
written 13.2 years ago by Steffen Durinck420
0
votes
1
answer
342
views
1
answers
Answer: A: RMAGEML: importMAGEOM returns nil pointer
... Hi Vincent, Which version of RMAGEML are you using. The latest versions (see developmental packages) all work without SJava. When you tried to import E-CAGE-2 did you also put the MAGE-ML document containing the Array design (A-MEXP-10) in the same directory? Best, Steffen Vincent Bloch wrote: ...
written 13.2 years ago by Steffen Durinck420

Latest awards to Steffen Durinck

No awards yet. Soon to come :-)

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 203 users visited in the last hour