User: James F. Reid

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James F. Reid120
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Posts by James F. Reid

<prev • 12 results • page 1 of 2 • next >
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Answer: A: is it possible to find sample batch # in CEL files?
... Hi Brian, On 24/01/13 13:23, Brian Tsai wrote: > Hi, > > I've been downloading raw CEL files from the gene expression omnibus, and > have been trying to process them -- i'd like to account for batch effect > when computing differential expression, but the authors didn't provide the & ...
written 6.7 years ago by James F. Reid120
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Answer: A: AnnotationForge example does not work
... Hi Nicos, I think installing 'org.Hs.eg.db' will solve the problem. It is a required package when you load your newly created custom annotation package. HTH J. On 27/11/12 20:22, Nicos Angelopoulos [guest] wrote: > > > Dear all, > > I am trying to reproduce the example from > & ...
written 6.9 years ago by James F. Reid120
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Comment: C: CDF for GeneChip miRNA 2 array - Is there a miRNA 3 CDF?
... Hi Stephen and James, a comment concerning the use (mature) microRNA names below. On 09/11/12 17:15, James W. MacDonald wrote: > Hi Stephen, > > On 11/9/2012 10:27 AM, Stephen Turner wrote: >> Thanks Jim. Yes, that is the initial goal, looking for differentially >> expressed m ...
written 6.9 years ago by James F. Reid120
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Comment: C: pam implementation
... Hi John, On 05/11/12 09:42, John Lande wrote: > thank you both for the answer. > > the point is that pamr lacks of a specific vignette as other bioc packages > so I was wondering if it was discontinued somehow. > > is there around a tutorial that explains pipelines of analysis and ...
written 7.0 years ago by James F. Reid120
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Answer: A: taqman versions
... Ciao Marco, On 24/10/12 18:40, Marco Fabbri wrote: > I am working with Taqman Microrna and I am using different versions of cards. > I am having problems with different version. Applied biosystem uses > its own code that refers to specific mirbase version. > I wonder if you are aware of ...
written 7.0 years ago by James F. Reid120
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Comment: C: get al microRNA target sites for a given gene
... Dear Javier, On 16/10/12 15:03, James W. MacDonald wrote: > Hi Javier, > > On 10/16/2012 3:06 AM, Javier P?rez Florido wrote: >> Hi James, >> Thanks for your reply. >> What I want is something like this: >> http://docs.bioinfo.cipf.es/projects/cellbase/wiki/Feature_ ...
written 7.0 years ago by James F. Reid120
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Answer: A: get gene targets from a specific microRNA
... Hi Yot, > > Hi All, > > I'm trying to get lists of gene targets from specific microRNAs, namely the > hsa-miRs and hsa-let-7s from the package targetscan.Hs.eg.db. > > So far, I can only see a way to do that by mapping all hsa-miRs into miR > family names first, then get gen ...
written 7.1 years ago by James F. Reid120
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Answer: A: Download problems from GEO
... Hi Hendrik, it looks like a problem at GEO, for the moment the files at the GEO site are pointing to: ftp://ftp-private.ncbi.nlm.nih.gov/pub/geo/DATA/SeriesMatrix/GSE508/ instead of the default ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/SeriesMatrix/GSE508/ Maybe they are doing some maintenance of som ...
written 7.3 years ago by James F. Reid120
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Comment: C: GEOquery, GSEMatrix parameter and lifecycle of GEO series data
... Dear Sean and Gustavo, I cannot reproduce this error. See below. On 27/06/12 16:54, Sean Davis wrote: > On Wed, Jun 27, 2012 at 11:38 AM, Gustavo Fern??ndez Bay??n > wrote: > >> Hi again. >> >> I would like to add a little bit more of information on this issue. I have & ...
written 7.3 years ago by James F. Reid120
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Comment: C: Printing arrayQualityMetrics report
... Hi, suggestion below On 21/06/12 23:02, Wolfgang Huber wrote: > Dear David > > I get a reasonable PDF with default settings on Firefox 13 on a Mac OS X > 10.6.8. I will send you this off-list. However, it is not perfect and > some twiddling with printer formating may improve things. ...
written 7.3 years ago by James F. Reid120

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