User: kaushal Raj Chaudhary

Reputation:
10
Status:
New User
Location:
United States
Last seen:
4 years, 2 months ago
Joined:
5 years, 9 months ago
Email:
k**********@gmail.com

Posts by kaushal Raj Chaudhary

<prev • 23 results • page 2 of 3 • next >
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Comment: C: Gene set enrichment analysis
... Hi Jim, I am trying to use geneSetTest() with t-value as statistics from top table.       geneSetTest(index=,   statistics=abs(tt$t), alternative="mixed", ranks.only=TRUE, nsim=9999) What values goes  in index argument? The documentation says  it is selected gene sets but I don't know which gene ...
written 4.6 years ago by kaushal Raj Chaudhary10
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Comment: C: Gene set enrichment analysis
... Hello Steve, I have gene expression data 28000 probes ( Affymetrix-rat) and 11 samples (case and control). I did run differential gene expression analysis using limma package but did not get significance based on the FDR values.  Now I want to perform gene set enrichment analysis  rather than indiv ...
written 4.6 years ago by kaushal Raj Chaudhary10
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Gene set enrichment analysis
... Hello Forum, I want to perform gene set enrichment analysis of whole genome. Can it be done or I have  to have some selective genes?  Thanks for any input in this regard.     ...
topgo gseabase gostat gsea written 4.6 years ago by kaushal Raj Chaudhary10 • updated 4.6 years ago by Levi Waldron950
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Comment: C: Subsetting ESet object based on featuredata
... Thanks, Jim. ...
written 4.7 years ago by kaushal Raj Chaudhary10
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Subsetting ESet object based on featuredata
... Hello all, I am trying to subset ESet object base on feature data.  Eset with with feature data was created using following code.   library(ragene10sttranscriptcluster.db) library(annotate) library(R2HTML) library(limma) ID <- featureNames(eset) Symbol <- getSYMBOL(ID, "ragene10sttrans ...
affy written 4.7 years ago by kaushal Raj Chaudhary10 • updated 4.7 years ago by James W. MacDonald50k
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Comment: C: Adjusted P vlaues
... Thanks, Jim.  ...
written 4.7 years ago by kaushal Raj Chaudhary10
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Comment: C: Adjusted P vlaues
... Hi Jim, I am filtering the genes at eset object. source("http://bioconductor.org/biocLite.R") biocLite("ragene10sttranscriptcluster.db")   biocLite("ALL") library(ragene10sttranscriptcluster.db) library(genefilter) annotation(eset) <- "ragene10sttranscriptcluster.db" celfiles.filt<- nsFilt ...
written 4.7 years ago by kaushal Raj Chaudhary10
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Adjusted P values
... Hello Forum, I am doing gene expression analysis using limma package.  After reducing the number of tests through filtering of genes, I am getting higher adjusted p values.  Just curious, what is causing this, probably no significant differences in signals. I appreciate any insight. Thanks, R co ...
genefilter limma written 4.7 years ago by kaushal Raj Chaudhary10 • updated 4.7 years ago by Gordon Smyth37k
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Comment: C: filter.log in nsFilter function (package genefilter) gives null value
... Thanks Jim. ...
written 4.8 years ago by kaushal Raj Chaudhary10
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Comment: C: filter.log in nsFilter function (package genefilter) gives null value
... Hi James, I  was  expecting  celfiles.filt$filter.log to be list of following objects like this. $numDupsRemoved [1] .... $numLowVar [1] ..... $feature.exclude [1] ...... In my case, I had originally  28826 features and after nsFIlter ing  they have been reduced to  8793 .   Thanks ! ...
written 4.8 years ago by kaushal Raj Chaudhary10

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Popular Question 4.2 years ago, created a question with more than 1,000 views. For Gene set enrichment analysis

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