User: Roopa Subbaiaih

gravatar for Roopa Subbaiaih
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4 years, 9 months ago
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6 years, 11 months ago
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Posts by Roopa Subbaiaih

<prev • 14 results • page 1 of 2 • next >
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A package to analyse Quantitative proteomics study
... Hi All, Is there a good package which analyses quantitative proteomics study, particularly label free approach? Please let me know. Thanks in advance, Roopa       ...
massspectrometry written 4.8 years ago by Roopa Subbaiaih130 • updated 4.8 years ago by Laurent Gatto1.2k
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Sciplot: Increasing the width of bargraph and decreasing the sapce b/n groups
... Hello, I am trying to plot bargraphs susing Sciplot. Is there a way to increase the width of the bar graphs and decrease the space b/n the groups? I am pasting the script as well as attaching the graph. Bio6 <- read.csv("Data/Plin1.csv",na.strings="",header=T) attach(Bio6) head(Bio6) par(family ...
graph written 5.3 years ago by Roopa Subbaiaih130 • updated 5.3 years ago by James W. MacDonald50k
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GAGE analysis
... Hi all, I was looking for good packages which does gene enrichment analysis. I came across GAGE which provides good analysis. My question is can it take up proteomics data too or is it designed for microarray data sets only. The data which I would like to analyze looks like this- Symbol Unaff (F ...
microarray gage written 5.6 years ago by Roopa Subbaiaih130 • updated 5.6 years ago by Luo Weijun1.5k
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Comment: C: LogFC query in Limma
... Dear Gordon, Thanks, I could complete the analysis. Roopa   ...
written 6.5 years ago by Roopa Subbaiaih130 • updated 4.8 years ago by Gordon Smyth38k
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LogFC query in Limma
... Hi James, Am I still making any silly mistake over here. I am comparing normal (21) with lesionous patient samples (34). This is what I get in R console. Is there a problem with the script? Any advice would greatly help for further analysis.Thanks, Roopa > getwd() [1] "C:/Documents and Setting ...
pathways cancer probe limma convert written 6.5 years ago by Roopa Subbaiaih130 • updated 6.5 years ago by Gordon Smyth38k
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Comment: C: LogFC query in Limma
... What you said was true. They are probe sets. When I upload the information into IPA 54k probe sets gives ~18k genes identified. I was concerned with fold changes for further analysis. Thanks, Roopa On Thu, Jan 31, 2013 at 4:02 PM, Steve Lianoglou < mailinglist.honeypot@gmail.com> wrote: ...
written 6.6 years ago by Roopa Subbaiaih130
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Comment: C: LogFC query in Limma
... Hi Steve, This was the script I used- getwd() setwd(dir="/CRSP 406-11/DEMOS/GSE14905-a") ls() #-----------------------------------------------# library(affy) eset = justRMA() f <- factor(c(1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1, 2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2 ...
written 6.6 years ago by Roopa Subbaiaih130
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LogFC query in Limma
... Hi All, Thanks for the reply, I could pull out the the whole information for differentially expressed genes. The criteria used was adjust="fdr", p=0.05. I came up with ~ 20,000 genes to be differentially expressed. Since I wanted to analyze these genes for deregulated pathways I had to come up wit ...
pathways convert written 6.6 years ago by Roopa Subbaiaih130 • updated 6.6 years ago by Steve Lianoglou12k
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Comment: C: Query regarding limma
... Thank you both. It worked. Roopa ...
written 6.6 years ago by Roopa Subbaiaih130 • updated 4.8 years ago by Gordon Smyth38k
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Query regarding limma
... Hi All, I was doing microarray analysis where I compare healthy with diseased samples. The script which I use is getwd() setwd(dir="/CRSP 406-11/DEMOS/GSE14905-a") ls() #-----------------------------------------------# library(affy) eset = justRMA() f <- factor(c(1,1,1,1,1,1,1,1,1,1,1,1,1,1,1, ...
microarray limma written 6.6 years ago by Roopa Subbaiaih130 • updated 4.8 years ago by Gordon Smyth38k

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Popular Question 4.8 years ago, created a question with more than 1,000 views. For LogFC query in Limma

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