User: Tim Smith

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Tim Smith1.0k
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Posts by Tim Smith

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Comment: C: Mapping gene symbols to gene names (org.Hs.eg.db?)
... Thanks Jim! On Tuesday, May 13, 2014 10:18 AM, James W. MacDonald wrote: Hi Tim, >symbols <- c('JAK1','AATK','A2BP1','A2LD1') >select(org.Hs.eg.db, symbols, c("ENTREZID","GENENAME"), "ALIAS")   ALIAS ENTREZID                                          GENENAME 1  JAK1    3716            ...
written 3.5 years ago by Tim Smith1.0k
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Mapping gene symbols to gene names (org.Hs.eg.db?)
... Hi, I was trying to map gene symbols to gene names using the org.Hs.eg.db package. I first convert the gene symbol to an entrez id, and then convert that to a gene name (example code below). However, during this process I can't get the gene names for some of the genes: -------------------------- ...
convert written 3.5 years ago by Tim Smith1.0k • updated 3.5 years ago by James W. MacDonald45k
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Comment: C: Genes annotated to GO:0031281 using org.Hs.eg.db
... Thanks Jim -  I think you've cracked it!! On Monday, March 24, 2014 12:01 PM, James W. MacDonald wrote: Hi Tim, Different approach. gos <- summary(hgOverGO)[,1] gIU <- geneIdUniverse(hgOverGO)[gos] gns <- geneIds(hgOverGO) golst <- lapply(gIU, function(x) x[x %in% gns]) And as ...
written 3.7 years ago by Tim Smith1.0k
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Comment: C: Genes annotated to GO:0031281 using org.Hs.eg.db
... Hi James, Thanks for that. However, the number of genes associated with the GO term with your code example, doesn't match the number of genes associated with that GO term with summary(hgOverGO): For example, my hgOverGO gives 43 genes annotated to the node: GOBPID Pvalue OddsRatio ExpCount Count ...
written 3.7 years ago by Tim Smith1.0k
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Comment: C: Genes annotated to GO:0031281 using org.Hs.eg.db
... Hi James, Hmmm....I seem to get an error if I use probeSetSummary. As I mentioned before I run the hyperGTest using a set of genes (and not a set of probes). Here is what I get: hgOverGO <- hyperGTest(paramsGO) > hgOverGO Gene to GO BP Conditional test for over-representation 3843 GO BP ...
written 3.7 years ago by Tim Smith1.0k
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Comment: C: Genes annotated to GO:0031281 using org.Hs.eg.db
... Hi James, Thanks for the reply! I had 371 genes ( gene universe ~ 7k genes) for which I was checking enrichment and I got this term as one of the significant terms. The details are:                GOBPID      Pvalue OddsRatio    ExpCount Count Size Term GO:0031281 0.021301601 10.113271  0.22913929 ...
written 3.7 years ago by Tim Smith1.0k
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Genes annotated to GO:0031281 using org.Hs.eg.db
... Hi, I was trying to get the genes annotated to the GO term "GO:0031281". My code: library(org.Hs.eg.db) genes <- get("GO:0031281", org.Hs.egGO2EG) When I run the code, I get: > genes <- get("GO:0031281", org.Hs.egGO2EG) Error in .checkKeys(value, Rkeys(x), x@ifnotfound) :   value for " ...
go homo sapiens written 3.7 years ago by Tim Smith1.0k • updated 3.7 years ago by James W. MacDonald45k
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Significance of overlapping GO terms?
... Hi, I had two sets of genes (say gset1 and gset2) drawn from a universe of N genes. I use GO to determine the terms that are enriched in gene set (say, GOterms1 and GOterms2). Is there a way that I can check the significance of the number of overlapping terms in GOterms1 & GOterms2 (i.e. signif ...
go written 3.7 years ago by Tim Smith1.0k
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OMIM - biomaRt?
... Hi, Sorry for the newbie question. Is it possible to get the disease phentoype information from OMIM using biomaRt or a similar package? For example, if I want to get the phenotypes associated with 'BRCA2' from OMIM, which function/package should I be looking at? Any help would be appreciated! th ...
biomart written 3.7 years ago by Tim Smith1.0k
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biomaRt: retrieve exon sequence, start and end positions
... Hi, I would like to retrieve the exon sequences (i.e. 5'UTR + CDS + 3'UTR) for a gene, alongwith the start and end positions for each exon. My short script is: ========= library(biomaRt) ## Example gene: MTOR; ensembl id "ENSG00000198793" mySequence <- getSequence(id="ENSG00000198793",type="e ...
written 3.9 years ago by Tim Smith1.0k • updated 3.9 years ago by Steffen Durinck530

Latest awards to Tim Smith

Centurion 3.5 years ago, created 100 posts.
Popular Question 3.5 years ago, created a question with more than 1,000 views. For biomaRt: retrieve exon sequence, start and end positions
Popular Question 3.5 years ago, created a question with more than 1,000 views. For org.Hs.eg.db -- Entrez ID to Gene Symbol conversion
Popular Question 3.5 years ago, created a question with more than 1,000 views. For Mapping gene symbols to gene names (org.Hs.eg.db?)
Popular Question 3.5 years ago, created a question with more than 1,000 views. For org.Hs.eg.db -- Entrez ID to Gene Symbol conversion
Popular Question 3.5 years ago, created a question with more than 1,000 views. For installing 'lme4' package fails

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