User: Aedin Culhane

gravatar for Aedin Culhane
Aedin Culhane510
Reputation:
510
Status:
Trusted
Location:
United States
Website:
http://www.hsph.harvar...
Scholar ID:
Google Scholar Page
Last seen:
10 months ago
Joined:
13 years, 4 months ago
Email:
a****@jimmy.harvard.edu

Dept of Biostatistics and Computational Biology, Dana Farber Cancer Institute, 

Dept of Biostatistics, Harvard School of Public Health

 

Packages: made4, mogsa, omicade4, iBBiG, RamiGO. 

Posts by Aedin Culhane

<prev • 70 results • page 2 of 7 • next >
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getBM. Get genome location for probes that do not map to genes
... Hi I am trying to get annotation on affy_hugene probes.  When I go to EnsEMBL, i can see these map unique to introns of genes.  Can I use getBM (biomaRt) to retrieve the genome location of mapped probes.   Then I can query other db to get annotation for that genomics region mart <- useDataset(" ...
annotation biomart written 2.5 years ago by Aedin Culhane510
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Comment: A: Constellation Map from the Broad?
... Hi Thanks, I know the Broad didn't provide an R package, but they provided R scripts so I was wondering if anyone else had made a package. Has anyone used  Constellation Map (even in GenePattern) and found it useful? Aedin ...
written 2.9 years ago by Aedin Culhane510
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Answer: A: Error while running piano's runGSA
... Hi Can you post a couple of rows/cols of gene.level.stats and also the first rows of gsc.  It looks like that the identifiers don't match. Aedin ...
written 2.9 years ago by Aedin Culhane510
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Answer: A: Prior Control with Mclust package
... Sorry mean to give example code With 5 cluster, G=1:5 testdata<-iris[,-5] tt<- mclustBIC(testdata, G = 1:5) plot(tt)   Default is 9 clusters.. G=1:9  plot(mclustBIC(testdata)) ...
written 2.9 years ago by Aedin Culhane510
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Answer: A: Prior Control with Mclust package
... Hi  Try specifying G. The default is 9.   G is an integer vector specifying the numbers of mixture components (clusters) for which the BIC is to be calculated. The default is G=1:9, unless the argument x is specified, in which case the default is taken from the values assoc ...
written 2.9 years ago by Aedin Culhane510
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Answer: A: Why are these two clustering patterns different?
... Hi It could be because aheatmap includes a scale or re-order function.  However looks     plot(hclust(dist(t(USArrests), method="euclidean"), "complete"), hang=-1) aheatmap(USArrests, distfun = "euclidean", hclustfun = "complete")    However when you have more than about 10 columns, aheatmap d ...
written 2.9 years ago by Aedin Culhane510
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Constellation Map from the Broad?
... Hi Just a quick question. I don't want to re-create a package if someone has one done already.  Has anyone tried or created an R package of the Broad's GSEA result visualization tool Constellation Map?   Had anyone tested this ok and run into problems? http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4 ...
gene set analysis written 2.9 years ago by Aedin Culhane510
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Answer: A: A very large number of diffential genes
... I have seen large number of differentially expressed genes if  1) Experimental design, for example there is a batch effect that is confounded with the biological effect, for example all controls were performed in one batch and all the treatment were performed in a separate batch. In this case the d ...
written 3.5 years ago by Aedin Culhane510
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Answer: A: What do ellipses in 'plotarrays' function represent (from made4)
... Oops sorry for posting twice. I'm not sure what I did wrong.  ...
written 3.5 years ago by Aedin Culhane510
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Answer: A: What do ellipses in 'plotarrays' function represent (from made4)
... Hi Maarten Sorry for the long wait for a reply, the ellipse is simply an inertia ellipse. Its just meant to highlight the individuals of the group and shows most of the group were projected within that location on the axes. It is not a confidence ellipse. To turn off the ellipse, set ellipse to 0. ...
written 3.5 years ago by Aedin Culhane510

Latest awards to Aedin Culhane

Popular Question 2.5 years ago, created a question with more than 1,000 views. For ReadAffy - Error VECTOR_ELT() can only be applied to a 'list', not a 'char'
Autobiographer 3.5 years ago, has more than 80 characters in the information field of the user's profile.

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