User: Aedin Culhane

gravatar for Aedin Culhane
Aedin Culhane510
Reputation:
510
Status:
Trusted
Location:
United States
Website:
http://www.hsph.harvar...
Scholar ID:
Google Scholar Page
Last seen:
3 months ago
Joined:
11 years, 10 months ago
Email:
a****@jimmy.harvard.edu

Dept of Biostatistics and Computational Biology, Dana Farber Cancer Institute, 

Dept of Biostatistics, Harvard School of Public Health

 

Packages: made4, mogsa, omicade4, iBBiG, RamiGO. 

Posts by Aedin Culhane

<prev • 69 results • page 1 of 7 • next >
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Comment: C: oligo and GenericPDInfo
... Hi Jim Ignore the last question. I was incorrect Aedin On 7/18/17 11:15, James W. MacDonald [bioc] wrote: > Activity on a post you are following on support.bioconductor.org > <https: support.bioconductor.org=""> > > User James W. MacDonald <https: support.bioconductor.org=" ...
written 3 months ago by Aedin Culhane510
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Comment: C: oligo and GenericPDInfo
... Hi Jim To make your function "happy", I need to specify the oligo version of the functions. backgroundCorrect was calling a limma function, normalize was calling a igraph function. It couldn't find basicAnnotatedDataFrame, as its not exported. When I modified the following lines, it worked ...
written 3 months ago by Aedin Culhane510
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Comment: C: oligo and GenericPDInfo
... Thanks I am very glad, I didn't spend the next few hours trying to work this out by myself... I don't think I would have got too far. Thanks for being so responsive. If oligo and brainarrays folks could get together to agree some standards, these great resources would be more accessible to the ...
written 3 months ago by Aedin Culhane510
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Comment: C: oligo and GenericPDInfo
... Thanks a million Jim oligo:::getMPSInfo is what I looking for. Since its not exported in the NAMESPACE, there is no help. Where can I find some additional info or help, for example a description of mps1, mps0 etc, as I see you use both below. The 'fields' parameter ("fid", etc). Aedin On ...
written 3 months ago by Aedin Culhane510
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oligo and GenericPDInfo
... Hi I have an old array that is not annotated within Bioc annotation.  I tried affy and oligo package, but am running into issues applying a non-standard (invariantset) normalization.   We have good bioloigcal reasons to believe that total transcriptional counts should vary in samples, so rma so I w ...
affy pdinfobuilder annotationdbi oligoclasses oligo package written 3 months ago by Aedin Culhane510 • updated 3 months ago by James W. MacDonald44k
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Answer: A: [FIXED] Error in Gviz (actually, rtracklayer) | IdeogramTrack
... Hi. Can you post your updated session info. It works ok on my mac Aedin ...
written 7 months ago by Aedin Culhane510
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Answer: A: [FIXED] Error in Gviz (actually, rtracklayer) | IdeogramTrack
... All fixed   ...
written 8 months ago by Aedin Culhane510
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Answer: A: getBM. Get genome location for probes that do not map to genes
... Thanks James EnsEMBL has already mapped all of the sequences to the genome (see http://useast.ensembl.org/Homo_sapiens/Location/Genome?fdb=funcgen;ftype=ProbeFeature;id=7893529;ptype=pset), so really I just want to pull their mappings.  But I couldn't work out how to do this with BiomaRt.  Do you k ...
written 12 months ago by Aedin Culhane510
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Answer: A: getBM. Get genome location for probes that do not map to genes
... BTW, I also tried  select(hugene10sttranscriptcluster.db, keys = "7893529", keytype = "PROBEID", columns="MAP") ...
written 12 months ago by Aedin Culhane510
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getBM. Get genome location for probes that do not map to genes
... Hi I am trying to get annotation on affy_hugene probes.  When I go to EnsEMBL, i can see these map unique to introns of genes.  Can I use getBM (biomaRt) to retrieve the genome location of mapped probes.   Then I can query other db to get annotation for that genomics region mart <- useDataset(" ...
annotation biomart written 12 months ago by Aedin Culhane510

Latest awards to Aedin Culhane

Popular Question 12 months ago, created a question with more than 1,000 views. For ReadAffy - Error VECTOR_ELT() can only be applied to a 'list', not a 'char'
Autobiographer 2.0 years ago, has more than 80 characters in the information field of the user's profile.

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