User: Jeremy Ng
Jeremy Ng • 170
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- 3 years ago
- Joined:
- 5 years, 10 months ago
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Posts by Jeremy Ng
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... A very quick workaround is to simply subset on the BiomartGeneRegionTrack
to contain feature information only on the specific transcript of interest
prior to plotting. This can be done by modifying the data directly as such:
biomTrack_hmgcr@range = biomTrack_hmgcr@range[biomTrack_hmgcr@range
$trans ...
written 13 months ago by
Jeremy Ng • 170
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... Does this work?
all_genes[!all_genes$GeneID%in%Genelist,]
Jeremy
On Wed, Jul 8, 2015 at 11:48 PM, ChIP-Tease [bioc] <noreply@bioconductor.org> wrote:
> Activity on a post you are following on support.bioconductor.org
>
> User ChIP-Tease <https: support.bioconductor.org="" u="" ...
written 3.0 years ago by
Jeremy Ng • 170
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... Hi Anita,
The ordering on the x-axis in ggplot is usually done alphabetically. There
are two ways which can be used to do this:
(1) You need to re-order the factors in the data.frame. This is done as
such:
d.f2$Sample <-
factor(d.f2$Sample,levels=c("WT-A6","WT-WT7","Re-WT2","Re-A1","Re-A3","Re- ...
written 3.1 years ago by
Jeremy Ng • 170
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... Hi James,
Thanks! that did the trick; turned out some of my Bioconductor packages
were out of date ...
Rgds,
Jeremy
On Fri, May 22, 2015 at 11:06 PM, James W. MacDonald [bioc] <
noreply@bioconductor.org> wrote:
> Activity on a post you are following on support.bioconductor.org
>
> ...
written 3.1 years ago by
Jeremy Ng • 170
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... Hi everyone,
I was trying to load BiocInstaller in order to install additional packages during my analysis, but this error message keeps returning:
library(BiocInstaller)
Error in unloadNamespace(package) :
namespace 'BiocInstaller' is imported by 'affy', 'oligoClasses' so cannot be unloaded
Er ...
written 3.1 years ago by
Jeremy Ng • 170
• updated 3.1 years ago by
James W. MacDonald ♦ 46k
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... Hi Steve, Michael and Malcolm,
Thanks very much for your suggestions.
I'd need to think about how to deal with these overlapping signals as
well
before I give Steve's suggestion a go!
Thanks again for your kind advice and guidance!
Jeremy
On Sat, Mar 22, 2014 at 6:02 AM, Michael Lawrence
wrote ...
written 4.3 years ago by
Jeremy Ng • 170
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... Hi there,
I'm relatively new to the GRanges class of objects, and have some
questions; and hopefully, I'd be able to better understand what's
going on
here.
I have 2 Granges objects, which are data from GEO. I want to find
where the
overlap, and then after that, the signals from each set. Here's w ...
written 4.3 years ago by
Jeremy Ng • 170
• updated 4.3 years ago by
Michael Lawrence ♦ 10.0k
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Comment:
C: limma-voom
... Hi,
Just wanted to add in a little more on the "normal" adjacent samples
that
TCGA uses.
I work with breast cancer samples, and it has appeared that some(if
not
many) of these "normal" adjacent samples are really similar to the
tumour
themselves. This has been reported earlier (see
http://cancerre ...
written 4.4 years ago by
Jeremy Ng • 170
0
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... hi there,
what you need is the huex10sttranscriptcluster.db for the HuEx 1.0
arrays.
I'm not sure if James had made it available for download from the BioC
site
yet.
Prior what I did was to use BiomaRt to fetch the probe ID, then look
used
the Affymetrix supplied annotation files (which I got fro ...
written 4.4 years ago by
Jeremy Ng • 170
0
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... Hi,
Try biocLite("pasilla") instead of install.packages() ? It worked for
me.
J
On Thu, Dec 19, 2013 at 12:21 PM, liyue [guest]
wrote:
>
> Hi,
>
> I try to install pasilla.
>
> > biocinstallRepos()
> > install.packages("pasilla")
> package âpasillaâ is not avai ...
written 4.5 years ago by
Jeremy Ng • 170
Latest awards to Jeremy Ng
Popular Question
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created a question with more than 1,000 views.
For Loading BiocInstaller fails when affy is loaded
Scholar
3.1 years ago,
created an answer that has been accepted.
For A: Delete all rows which contain a GeneID from a list with several GeneIDs
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