User: Gad Abraham

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Gad Abraham110
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Posts by Gad Abraham

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Comment: C: GEOquery not working, NCBI changes?
... On Thu, Mar 4, 2010 at 12:39 PM, Gad Abraham wrote: > On Wed, Mar 3, 2010 at 8:04 PM, Sean Davis wrote: >> On Wed, Mar 3, 2010 at 6:32 AM, Gad Abraham >> wrote: >>> Hi, >>> >>> I'm having trouble getting GEOquery to work recently. >>> >>> ...
written 9.4 years ago by Gad Abraham110
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Comment: C: GEOquery not working, NCBI changes?
... On Wed, Mar 3, 2010 at 8:04 PM, Sean Davis wrote: > On Wed, Mar 3, 2010 at 6:32 AM, Gad Abraham > wrote: >> Hi, >> >> I'm having trouble getting GEOquery to work recently. >> >> On Ubuntu 9.10/R-2.10.1/BioC 2.6.1, GEOquery 2.11.3, download.file >> stops wi ...
written 9.4 years ago by Gad Abraham110
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GEOquery not working, NCBI changes?
... Hi, I'm having trouble getting GEOquery to work recently. On Ubuntu 9.10/R-2.10.1/BioC 2.6.1, GEOquery 2.11.3, download.file stops with "cannot open URL", On Ubuntu 8.04.1/R-2.9.2/BioC 2.4.1, GEOquery 2.8.0, curlPerform stops with "Server denied you to change to the given directory" wget download ...
geoquery written 9.4 years ago by Gad Abraham110 • updated 9.4 years ago by Sean Davis21k
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Finding longest transcript
... Hi, I've got some Affy U133A data, and I'd like to find out for each gene, which probeset represents the longest transcript. Is there a nice way to do this in BioC/BiomaRt? Thanks, Gad -- Gad Abraham PhD Student, Dept. CSSE and NICTA The University of Melbourne Parkville 3010, Victoria, Australi ...
affy written 9.6 years ago by Gad Abraham110
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Comment: C: OT: van 't Veer (2002) classifier
... On 12/08/09 1:02 AM, Francois Pepin wrote: > Hi Gad, > > I don't know of a reference implementation for this. The differences you > explain depend on whether you want a more specific or a more sensitive > classifier. As you mentioned, different variations have been used in the > di ...
written 9.9 years ago by Gad Abraham110
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OT: van 't Veer (2002) classifier
... A non-BioC question: Does anyone know of an authoritative implementation of the van 't Veer et al (2002) breast cancer metastasis classifier? There seem to be different interpretations in the literature, in some places (e.g., van de Vijver 2002, Tibshirani & Efron 2002, Mansmann et al2006) it' ...
classification cancer breast written 10.0 years ago by Gad Abraham110 • updated 10.0 years ago by Francois Pepin1.3k
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RefSeq summary from biomaRt
... On 26/6/09 7:00 PM, Sean Davis wrote: > Hi, Gad. I'm not sure what your goal is for looking for such genes, but > I think it likely that nearly all genes undergo alternative splicing > under the right conditions, so any gene that has multiple transcripts in > a database like RefSeq (or ...
microarray written 10.1 years ago by Gad Abraham110
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Comment: C: RefSeq summary from biomaRt
... On 26/6/09 2:15 PM, Steve Lianoglou wrote: > Hi, > > On Jun 25, 2009, at 11:43 PM, Gad Abraham wrote: > >> Hi, >> >> Is it possible to get RefSeq summaries for a given gene using biomaRt >> (or any other tool?) From ensembl I can only get RefSeq DNA ID, RefSeq > ...
written 10.1 years ago by Gad Abraham110
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RefSeq summary from biomaRt
... Hi, Is it possible to get RefSeq summaries for a given gene using biomaRt (or any other tool?) From ensembl I can only get RefSeq DNA ID, RefSeq Predicted DNA ID, RefSeq Protein ID, RefSeq Predicted Protein ID. Specifically, I'm looking for mentions of alternative splicing (e.g., "Alternatively sp ...
written 10.1 years ago by Gad Abraham110 • updated 10.1 years ago by Steve Lianoglou12k
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Answer: A: GEOquery::parseGEO throws error reading file
... Sean Davis wrote: > On Sun, Jul 27, 2008 at 11:44 PM, Gad Abraham > wrote: >> Hi, >> >> I'm using GEOquery 2.4.1 to read an NCBI GEO file >> ftp://ftp.ncbi.nih.gov/pub/geo/DATA/SeriesMatrix/GSE4284/GSE4284_se ries_matrix.txt.gz >> but parseGEO throws an error. T ...
written 11.0 years ago by Gad Abraham110

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