User: Hari Easwaran

gravatar for Hari Easwaran
Hari Easwaran240
Reputation:
240
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Location:
United States
Last seen:
4 years, 1 month ago
Joined:
10 years, 1 month ago
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h***********@gmail.com

Posts by Hari Easwaran

<prev • 24 results • page 1 of 3 • next >
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Answer: A: ChIPpeakAnno: findOverlapsOfPeaks keep GRanges metadata
... Hi Jianhong, Thanks for your message. It works now. Earlier I had a problem with R3.2 in that it could not find BiocParallel, and I could not install it. Had to restart R and reinstall Bioconductor, ChIPpeakAnno, BiocParallel.... it works now. Thanks.   ...
written 4.2 years ago by Hari Easwaran240
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Answer: A: ChIPpeakAnno: findOverlapsOfPeaks keep GRanges metadata
... I am facing a weird problem with ChIPpeakAnno. I am  to able to fine the function findOverlapsOfPeaks. I get the following: > findOverlapsOfPeaks Error: object 'findOverlapsOfPeaks' not found However, other functions like annotatePeakInBatch can be found. Any idea what could be wrong. Thanks ...
written 4.2 years ago by Hari Easwaran240
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Comment: C: biomaaRt error: Extra content at the end of the document
... Hi Steffen, Thanks for your help. Sincerely, Hari On Thu, Jan 16, 2014 at 12:38 PM, Steffen Durinck wrote: > Hi Hari, > > If you go to the web page of BioMart for that specific archive you'll see > that is temporarily unavailable. > > http://may2009.archive.ensembl.org/biomar ...
written 5.5 years ago by Hari Easwaran240
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biomaaRt error: Extra content at the end of the document
... Hi all, I am facing a problem with biomaRT which was working fine until yesterday. This is what I ma doing: library(biomaRt) library(RCurl) ensembl54 = useMart(host="may2009.archive.ensembl.org", biomart="ENSEMBL_MART_ENSEMBL", dataset="hsapiens_gene_ensembl") #Get the hg18 version in biomart I am ...
biomart written 5.5 years ago by Hari Easwaran240 • updated 5.5 years ago by Steffen Durinck540
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Comment: C: Advice on reading big BED/BAM and ChIP-seq quality control
... Hi Martin, Steve, and Michael, I have to do some homework reading the vignettes and working on a small subset. Michael, I came across QuasR in my search. Will try that. If I got it, Rsamtools, as well as QuasR, allows reading part of the data, say for a chromosome, thus helping in managing memory i ...
written 6.2 years ago by Hari Easwaran240
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Advice on reading big BED/BAM and ChIP-seq quality control
... Dear Bioc gurus, I am a newbie with using R tools for ChIP-seq analyses and seek advice on the best way to go about a data set I have. Following are the file formats I have and what I would like to do with them: 1) Using Samtools, I created BED files (about 5 Gb) from the BAM files (3-4 Gb) 2) W ...
go rtracklayer rsamtools written 6.2 years ago by Hari Easwaran240 • updated 6.2 years ago by Michael Stadler330
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Comment: C: annotation package for Agilent Human GE 4x44K v2 (catalog # G4845A)
... Thanks Jim. I saw a paper using hgug4110b.db, hence wanted to clarify. I could not find the annotation file in the Agilent website. Anyways, thanks for your help. Hari On Tue, Aug 7, 2012 at 1:27 PM, James W. MacDonald wrote: > Hi Hari, > > > On 8/7/2012 12:30 PM, Hari Easwaran wrot ...
written 7.0 years ago by Hari Easwaran240
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annotation package for Agilent Human GE 4x44K v2 (catalog # G4845A)
... Dear all, Is the annotation package for Agilent Human GE 4x44K v2 (catalog # G4845A) array available in Bioconductor. I am not sure if "hgug4110b.db" is the one I am looking for. Can someone help? Thanks is advance. Hari [[alternative HTML version deleted]] ...
annotation written 7.0 years ago by Hari Easwaran240 • updated 7.0 years ago by James W. MacDonald50k
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Comment: C: Normalization for use of individual channels from 2-color arrays?
... Hi Sean, So it is fine to have the log ratios normalized before the data is subject to Aquantile normalization? Thanks for your help. Hari On Tue, Sep 13, 2011 at 10:43 AM, Sean Davis wrote: > On Tue, Sep 13, 2011 at 10:35 AM, Hari Easwaran > wrote: > > Dear BioC gurus, > > ...
written 7.9 years ago by Hari Easwaran240
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Normalization for use of individual channels from 2-color arrays?
... Dear BioC gurus, I am trying to use the individual channels from a 2-color array as a measure of gene expression level following the scripts in the Limma User Guide. The code the guide suggests is: MA <- normalizeBetweenArrays(MA, method="Aquantile") Throughout the guide, MA is an objected cr ...
normalization limma written 7.9 years ago by Hari Easwaran240 • updated 7.9 years ago by Sean Davis21k

Latest awards to Hari Easwaran

Popular Question 4.1 years ago, created a question with more than 1,000 views. For annotation package for Agilent Human GE 4x44K v2 (catalog # G4845A)
Popular Question 4.1 years ago, created a question with more than 1,000 views. For biomaaRt error: Extra content at the end of the document
Popular Question 4.1 years ago, created a question with more than 1,000 views. For Advice on reading big BED/BAM and ChIP-seq quality control
Popular Question 4.1 years ago, created a question with more than 1,000 views. For biomaaRt error: Extra content at the end of the document

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