User: Jeremy Ng

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Jeremy Ng170
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Posts by Jeremy Ng

<prev • 18 results • page 1 of 2 • next >
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Answer: A: Selecting only one transcript in BiomartGeneRegionTrack
... 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 $trans ...
written 6 months ago by Jeremy Ng170
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Answer: A: Delete all rows which contain a GeneID from a list with several GeneIDs
... Does this work? all_genes[!all_genes$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 2.4 years ago by Jeremy Ng170
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Answer: A: gene expression visualization: lineplot with ggplot2
... 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 2.5 years ago by Jeremy Ng170
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Comment: C: Loading BiocInstaller fails when affy is loaded
... 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 that did the trick; turned out some of my Bioconductor packages were out of date ...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 2.5 years ago by Jeremy Ng170
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Loading BiocInstaller fails when affy is loaded
... 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 ...
biocinstaller written 2.5 years ago by Jeremy Ng170 • updated 2.5 years ago by James W. MacDonald45k
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Comment: C: Question about working with GRanges objects
... 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 3.7 years ago by Jeremy Ng170
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Question about working with GRanges objects
... 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 ...
go written 3.7 years ago by Jeremy Ng170 • updated 3.7 years ago by Michael Lawrence9.8k
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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 3.8 years ago by Jeremy Ng170
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Comment: C: howto map HuEx-1_0-st-v2 transcript_cluster_id's to gene symbols
... 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 3.8 years ago by Jeremy Ng170
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Answer: A: package � pasilla� is not available (for R version 3.0.2)
... 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 ‘pasilla’ is not avai ...
written 3.9 years ago by Jeremy Ng170

Latest awards to Jeremy Ng

Popular Question 2.5 years ago, created a question with more than 1,000 views. For Loading BiocInstaller fails when affy is loaded
Scholar 2.5 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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