User: James F. Reid
James F. Reid • 120
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Posts by James F. Reid
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... 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 6.6 years ago by
James F. Reid • 120
0
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1
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... 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 6.7 years ago by
James F. Reid • 120
0
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... 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 6.8 years ago by
James F. Reid • 120
0
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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 6.8 years ago by
James F. Reid • 120
0
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1
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450
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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 6.8 years ago by
James F. Reid • 120
0
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1
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... 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 6.8 years ago by
James F. Reid • 120
0
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1
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... 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 6.9 years ago by
James F. Reid • 120
0
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1
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1.4k
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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 7.1 years ago by
James F. Reid • 120
0
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1
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... 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 7.1 years ago by
James F. Reid • 120
0
votes
1
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457
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... 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 7.2 years ago by
James F. Reid • 120
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