User: ivan.borozan@utoronto.ca

Reputation:
80
Status:
New User
Location:
Last seen:
12 years, 6 months ago
Joined:
15 years, 6 months ago
Email:
i***********@utoronto.ca

Posts by ivan.borozan@utoronto.ca

<prev • 8 results • page 1 of 1 • next >
0
votes
2
answers
1.1k
views
2
answers
Comment: C: hyperGTest, KEGG
... Hi Seth, Thanks I found one way around my problem (for the non devel version of the package Category): geneIds(hgOver)[geneIds(hgOver) %in% hgOver at catToGeneId[[i]]] where [[i]] runs over significant KEGG terms obtained from hyperGTest(params). Cheers, Ivan Quoting Seth Falcon : > Hi I ...
written 12.5 years ago by ivan.borozan@utoronto.ca80
0
votes
2
answers
1.1k
views
2
answers
hyperGTest, KEGG
... Hi, I've used the script below to calculate over-represented KEGG categories however I can not get to gene ID's associated with each of the overrepresented KEGG terms/pathways ? hgCutoff <- 0.01 params <- new("KEGGHyperGParams", geneIds = selectedEntrezIds, universeGeneIds = entrezUniverse ...
annotation pathways multtest siggenes rbgl gostats written 12.5 years ago by ivan.borozan@utoronto.ca80 • updated 12.5 years ago by Seth Falcon7.4k
0
votes
2
answers
686
views
2
answers
Comment: C: GOstats hyperGTest question
... Hi Seth, Thanks for your replay I actually had duplicates in my gene universe. Running hyperGTest now (without duplicates) gives meaningful results. all the best, Ivan Quoting Seth Falcon : > Hi Ivan, > > ivan.borozan at utoronto.ca writes: >> I got following results using hyperGTe ...
written 12.7 years ago by ivan.borozan@utoronto.ca80
0
votes
2
answers
686
views
2
answers
GOstats hyperGTest question
... Hi all, I got following results using hyperGTest(params) with a given list of genes > summary(hgOver) GOBPID Pvalue OddsRatio ExpCount Count Size 1 GO:0030185 0.000000e+00 -73.314685 0.02692165 2 1 2 GO:0006067 0.000000e+00 -110.746479 0.05384330 3 2 3 GO: ...
biobase annotate genefilter multtest graph written 12.7 years ago by ivan.borozan@utoronto.ca80 • updated 12.7 years ago by Seth Falcon7.4k
0
votes
0
answers
433
views
0
answers
question about the GeneMeta package
... hi there, How should i interpret the Qpvalues calculated in GeneMeta package once i've fitted an REM model to my data showing inhomogeneity of study effects with mean(Q_data)=6.27 and expected mean(Q_Chisq(df) = 3) = 2.9 ? all the best, ivan ...
genemeta written 14.3 years ago by ivan.borozan@utoronto.ca80
0
votes
0
answers
447
views
0
answers
question about multtest v.1.5.2
... Hi there, in multtest v.1.5.2 if i do resT<-mt.maxT(mattest,cl,B=100) ord<-order(resT$index) rawp<-resT$rawp[ord] maxT<-resT$adjp[ord] i get for data that are not available (i.e NA's) rawp[1] [1] NA maxT[1] [1] NA ...ect instead of rawp[1] [1] 3.402823e+38 maxT[1] [1] 3.402823e+38 ...
0
votes
0
answers
362
views
0
answers
question about plot dendrogram
... hi all, i'm trying to plot a dendrogram with labeled leaves >rownames(f)<-v.names >v<-rowMeans(f, na.rm=T) >clust<-hclust(dist(v)) >dend<-as.dendrogram(clust,hang=0.05) >clust2<-cut(dend, h=0.5) >class(clust2$low[[1]]) >[1] "dendrogram" then >plot(clust2$l ...
written 15.4 years ago by ivan.borozan@utoronto.ca80
0
votes
2
answers
479
views
2
answers
limma question
... hi there, I would like to estimate the effect on gene expression levels of two factors Age and activity (each with 4 levels) using Limma. for my design matrix i have dataB<-data.frame(samples = arrays,Age=factor(FFAge),activity = factor(FFfibrosis)) design<-model.matrix(~activity*Age, data ...
limma written 15.5 years ago by ivan.borozan@utoronto.ca80 • updated 15.5 years ago by Gordon Smyth38k

Latest awards to ivan.borozan@utoronto.ca

Popular Question 12.5 years ago, created a question with more than 1,000 views. For hyperGTest, KEGG

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 297 users visited in the last hour