User: peter robinson

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Posts by peter robinson

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Comment: C: Retrieving Upstream Sequences With biomaRt
... On Mon, Feb 26, 2007 at 09:08:50AM -0500, Steffen Durinck wrote: > Hi Peter, > > As many of you noticed recently the implementation of the getSequence > function in MySQL mode and in the default webservice mode is different. > In MySQL mode you can only retrieve sequences based on chr ...
written 12.7 years ago by peter robinson300
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Comment: C: Retrieving Upstream Sequences With biomaRt
... On Tue, Feb 20, 2007 at 12:11:02PM -0000, Stephen Henderson wrote: > The first code that you show doesn't work--for many reasons. > > >library(biomaRt) > >ens<-useMart("ensembl",dataset="hsapiens_gene_ensembl", mysql=TRUE) > >entrez <- c("100","330") > >gene <- ...
written 12.7 years ago by peter robinson300
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Retrieving Upstream Sequences With biomaRt
... Hi Conductors, I have been experimenting with the very nice biomaRt package and noticed in the vignette (section 5) that sequence retrieval appears to be restricted to the cDNA (possibly only UTR) or peptide sequences. From an earlier posting on the mailing list, I saw a way to retrieve upstream se ...
biomart written 12.8 years ago by peter robinson300 • updated 12.8 years ago by Stephen Henderson1.0k
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Differentially Expressed Genes in Time Series with Replications
... Dear list, I was wondering if anyone has some advice as to the best way of determining a list of DE genes for each time point of a series of experiments in which there are no replicates. (I am looking at the Spellman Yeast Cell Cycle data). On the one hand I am familiar with some methods such as t ...
yeast cycle written 12.8 years ago by peter robinson300
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Comment: C: GO enrichment for genome-wide analysis
... (... snip...) > > > > http://david.niaid.nih.gov/david/ease.htm > > Note that if you do use the above link, it will typically ask for a > "background" set; this is meant to be a prompt to the user to think about > what the actual background set should be. I realize that I ma ...
written 13.9 years ago by peter robinson300
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Error in bioClite instructions
... Dear list, on the page http://www.bioconductor.org/docs/install-howto.html the command biocLite(c("pkg1", "pkg2")) is recommended to install pkg1 and pkg2. On my system (linux, R 2.1, Bioconductor 1.6), this gives an error: > biocLite(c=("affyPLM")) Running bioCLite version 0.1 with R versi ...
written 14.3 years ago by peter robinson300 • updated 14.3 years ago by Benilton Carvalho4.3k
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Answer: A: GOStat and multiple testing
... Dear List, in light of the recent discussion on multiple testing in GO analysis, a project we recently finished may be of interest to some members of the list: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&d opt=Abstract&list_uids=15254011&itool=iconabstr We t ...
written 15.3 years ago by peter robinson300
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repos tools
... Dear List, I realize that problems surrounding getBioC have been discussed before, but the discussion do not seem to be relevant to my question. I am running a Debian Sarge system and R 1.91 installed as a debian package. When I enter >source("http://www.bioconductor.org/getBioC.R") >getBioC( ...
repostools written 15.3 years ago by peter robinson300
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[Re] Filtering by Fold Change
... Thanks to all who have sent comments and suggestions. I would like to ask one more question. I am doing the filtering to prepare a dataset for some several class discovery methods that blow up with relatively large datasets. I have about 60 tumor samples coming from 7 known biological classes, but c ...
normalization written 15.4 years ago by peter robinson300
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Filtering by fold change
... Dear List, I guess this is a pretty basic question, but I have not found an answer in the archives. I would like to take a matrix representing m hybridizations and sort it to extract the 2000 genes with the maximal fold change as a preliminary step of a further analysis. Is it possible to use the g ...
written 15.4 years ago by peter robinson300 • updated 15.4 years ago by Kasper Daniel Hansen630

Latest awards to peter robinson

Popular Question 10.3 years ago, created a question with more than 1,000 views. For Filtering by fold change
Popular Question 10.3 years ago, created a question with more than 1,000 views. For Cannot load preprocessCore.so
Popular Question 10.3 years ago, created a question with more than 1,000 views. For Affymetrix probeset ids to gene symbols
Popular Question 10.3 years ago, created a question with more than 1,000 views. For How to go from affymetrix to Ensembl transcript IDs
Popular Question 10.3 years ago, created a question with more than 1,000 views. For Differential expression in time series
Popular Question 10.3 years ago, created a question with more than 1,000 views. For Mapping Agilent Probes

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