User: Neel Aluru

gravatar for Neel Aluru
Neel Aluru450
Reputation:
450
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Trusted
Location:
United States
Last seen:
2 years, 9 months ago
Joined:
9 years, 10 months ago
Email:
n*****@whoi.edu

Posts by Neel Aluru

<prev • 49 results • page 1 of 5 • next >
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Comment: C: DEXSeqHTML parallelization error
... Hi Alejandro, Thanks for the reply. I ran the analysis on a Mac Pro (12-Core Intel Xeon E5, 2.7 GHz, 64 GB memory and 1TB hard drive; there is 250GB free space). I will try to run it on a server as you suggested. Thank you, Neel ...
written 3.8 years ago by Neel Aluru450
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Comment: C: DEXSeqHTML parallelization error
... I repeated it without BPPARAM and I am still getting the same error! ...
written 3.8 years ago by Neel Aluru450
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DEXSeqHTML parallelization error
... Hello, I am trying to generate HTML report for DEXSeq results and encountering parallelization error (at least I think it is a parallelization error). Any help in solving this problem will be highly appreciated. Thank you, Neel Here is my code and session Info() >library("DEXSeq") >setwd( ...
dexseq parallel dexseqhtml written 3.8 years ago by Neel Aluru450
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Comment: A: Unable to read data using readBismark in BiSeq
... I noticed that the "system.file" is not working. > file=system.file("CpG_zr1121_9.bismark.cov", package="BiSeq") > file "" # It is returning an empty vector! Is there something wrong in the command? Thanks, Neel ...
written 3.9 years ago by Neel Aluru450
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Unable to read data using readBismark in BiSeq
... I apologize for asking a very naive question. I am using BiSeq for the first time and I am having a hard time reading the data. readBismark command seems to be stalled. Any advice would be highly appreciated. Here is what I am trying to do. > library(BiSeq) Loading required package: GenomicRang ...
biseq readbismark written 3.9 years ago by Neel Aluru450 • updated 3.9 years ago by James W. MacDonald51k
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Comment: C: heatmap.2 Z-score vs logFC
... Thank you so much for clarifying. It makes total sense. Neel On 10/18/11 11:44 AM, Sean Davis wrote: > Hi, Neel. > > Some rows have larger logFC than others. Without scaling, those rows > will be brighter than the rows that have smaller logFC. Scaling the > rows (columns) makes th ...
written 7.9 years ago by Neel Aluru450
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heatmap.2 Z-score vs logFC
... Hello Bioc Users, I am having a hard time understanding why heatmap.2 uses row (or column) Z-score instead of directly plotting logFC values? Based on the formula for calculating Z-score, I understand that it is used for scaling or smoothing. But, isn't it the same when using logFC. Please correct ...
written 7.9 years ago by Neel Aluru450 • updated 7.9 years ago by Sean Davis21k
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Comment: C: edgeR: calcNormFactors
... Hi Naomi, I think this error is associated with old version of edgeR. Try upgrading to the latest version of edgeR. That's how I was able to get rid of it. Neel On Mar 11, 2011, at 3:24 PM, Jo?o Moura wrote: > Hi Naomi, > > just use as.matrix(TotalReads) instead ;) > > Cheers > ...
written 8.5 years ago by Neel Aluru450
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Comment: C: GGtools and GGBase installation problems
... Thank you, Vincent. It installed Ruuid from the command line. Earlier, I was trying to install Ruuid using R Gui and it doesn't work. Thanks a lot. Neel On Mar 3, 2011, at 6:40 AM, Vincent Carey wrote: > if you used fink, glib-config should be in /sw/bin -- check. then > make sure /sw/bin ...
written 8.5 years ago by Neel Aluru450
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GGtools and GGBase installation problems
... Hi Vincent, Thanks for the following guidelines. I followed the instructions and I still have the problem. I restarted the computer after installing Fink. Any help is appreciated. Thank you, Neel Here is what I get: > source("http://bioconductor.org/biocLite.R") BioC_mirror = http://www.bio ...
infrastructure gui ruuid ggtools ggbase written 8.5 years ago by Neel Aluru450 • updated 8.5 years ago by Vincent J. Carey, Jr.6.3k

Latest awards to Neel Aluru

Popular Question 2.7 years ago, created a question with more than 1,000 views. For SOLiD color space data
Great Question 2.7 years ago, created a question with more than 5,000 views. For heatmap.2 Z-score vs logFC
Popular Question 7.9 years ago, created a question with more than 1,000 views. For heatmap.2 Z-score vs logFC

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