User: Coghlan, Avril

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Posts by Coghlan, Avril

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breastCancerMAINZ package installation problem
... Dear all, I am trying to install the breastCancerMAINZ package but when I type: source("http://bioconductor.org/biocLite.R") biocLite("breastCancerMAINZ") as described on the webpage http://watson.nci.nih.gov/bioc_mirror/packages/2.8/data/experiment/htm l/ breastCancerMAINZ.html I get an er ...
written 7.7 years ago by Coghlan, Avril190 • updated 7.7 years ago by Martin Morgan ♦♦ 24k
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biomaRt package: problem with useDataset() function
... Dear all, I am trying to use the biomaRt package to retrieve data from the Ensembl database. However, I get an error message using the useDataset() function. I think this is perhaps because useDataset() does not expect Ensembl datasets to have spaces in their names, but some do. I have typed the f ...
biomart written 8.5 years ago by Coghlan, Avril190 • updated 8.5 years ago by Hotz, Hans-Rudolf400
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booklet on using R for biomedical statistics
... Dear Jp, Thank you for your email. I'm afraid I haven't written a chapter for survival analysis. I will think about that for the future. Regards, Avril -----Original Message----- From: Jin, Jp [mailto:jjin@email.unc.edu] Sent: 13 December 2010 15:57 To: Coghlan, Avril; bioconductor at r-project.o ...
survival written 8.9 years ago by Coghlan, Avril190
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Comment: C: booklet on using R for biomedical statistics
... Dear Vincent, Sorry about that.. I had thought it could be of interest to people on this list. Regards, Avril -----Original Message----- From: Vincent Carey [mailto:stvjc@channing.harvard.edu] Sent: 13 December 2010 15:06 To: Richard Friedman Cc: Coghlan, Avril; bioconductor at r-project.org Subj ...
written 9.0 years ago by Coghlan, Avril190
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booklet on using R for biomedical statistics
... Dear all, I've written a small booklet on using R for biomedical statistics (mostly focussed on cohort and case-control studies), available here under a Creative Commons Attribution 3.0 License : "A Little Book of R for Biomedical Statistics" http://a-little-book-of-r-for-biomedical-stati ...
written 9.0 years ago by Coghlan, Avril190 • updated 9.0 years ago by Jianping Jin890
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feature request - pairwiseAlignment() in Biostrings
... Dear Patrick and Steve, I am wondering whether it would be possible to add an option to the pairwiseAlignment() function in Biostrings, so that it could print out: (i) all the top-scoring alignments for 2 sequences, if there are more than one equally scoring top-scoring alignments ? (ii) the top X ...
biostrings written 9.4 years ago by Coghlan, Avril190 • updated 9.4 years ago by Patrick Aboyoun1.6k
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Comment: C: unexpected behaviour of pairwiseAlignment() in Biostrings
... Dear Patrick and Steve, Thank you for your helpful replies. I think that perhaps the problem was that I was using an old version of R (R 2.10). I had tried to update the Biostrings library by typing: >source("http://bioconductor.org/biocLite.R" >biocLite("Biostrings") >library("Biostrings ...
written 9.4 years ago by Coghlan, Avril190
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Answer: A: unexpected behaviour of pairwiseAlignment() in Biostrings
... Dear Patrick, I've updated my copy of the Biostrings() library but the pairwiseAlignment() function doesn't seem to have been fixed yet - I wonder could you send me the patch directly please? Kind Regards, Avril ________________________________ From: Patrick Aboyoun [mailto:paboyoun@fhcrc.org] S ...
written 9.4 years ago by Coghlan, Avril190
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unexpected behaviour of pairwiseAlignment() in Biostrings
... Dear Patrick, all, I have noticed what I think may perhaps be a bug in the pairwiseAlignment() function in Biostrings. I want to use it to calculate the optimal pairwise alignment between these two strings: s1 = "TCAGTTGCCAAACCCGCT" s2 = "AGGGTTGACATCCGTTTT" I want to use a match score of 10, a mis ...
alignment biostrings written 9.4 years ago by Coghlan, Avril190
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calculating heterozygosity, and genetic diversity
... Dear all, I am wondering is it possible to calculate allele frequencies, observed heterozygosity, expected Heterozygosity, and genetic diversity (Nei's genetic diversity) using Bioconductor? I have a set of microsatellite genotype data for a large number of microsatellite loci for diploid individua ...
written 9.7 years ago by Coghlan, Avril190 • updated 3.3 years ago by wangyizhusss0

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