User: anna freni sterrantino

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Posts by anna freni sterrantino

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Answer: A: Most stable gene pairs in array experiment
... Hi David, not sure what do you mean with stable, but you might be interested in correlation, a=matrix(sample(1:100),4,5) rownames(a)=paste("gene", letters[1:4]) colnames(a)=paste("cond", letters[1:5]) >a cond a cond b cond c cond d cond e gene a 95 31 3 9 93 gene b 1 ...
written 10.0 years ago by anna freni sterrantino120
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Answer: A: How to decide which distance metric to use for micoarray data clustering?
... Hi Peng, As long I'm concerned about your issue, I guess that you can choose any metric that you can interpret easily once you have done your analysis. But I think that for clustering microarray genes, ( I guess it's also suggested in the book you mention, which I don't have right here) a good solut ...
written 10.0 years ago by anna freni sterrantino120
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Answer: A: GO package
... Hi Joanna, GO package names has been changed to GO.db, I guess more than a year ago. Cheers Anna Anna Freni Sterrantino Ph.D Student Department of Statistics University of Bologna, Italy via Belle Arti 41, 40124 BO. ________________________________ Da: Joanna Zyprych A: bioconductor@stat.m ...
written 10.4 years ago by anna freni sterrantino120
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Answer: A: problem with "ls" command
... Hi, If you have installed KEGG.db correctly as: source("http://bioconductor.org/biocLite.R") biocLite("KEGG.db") and then in an R session you can type library("KEGG.db") ls("package:KEGG.db") [1] "KEGG" "KEGG_dbconn" "KEGG_dbfile" "KEGG_dbInfo" [5] "KEGG_dbschema" "KEGGENZY ...
written 10.4 years ago by anna freni sterrantino120
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Answer: A: function error
... Hi Renata, can you provide you sessionInfo() and a reproducible example? thanks Anna Anna Freni Sterrantino Ph.D Student Department of Statistics University of Bologna, Italy via Belle Arti 41, 40124 BO. ________________________________ Da: Renata Paiva A: bioconductor@stat.math.ethz.ch In ...
written 10.4 years ago by anna freni sterrantino120
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Answer: A: Packages not getting installed
... Hi, you are running an old R version, the actual one is R-2.9 and therfore new Bioc release have to be updated. Cheers Anna Anna Freni Sterrantino Ph.D Student Department of Statistics University of Bologna, Italy via Belle Arti 41, 40124 BO. ________________________________ Da: Ashwin Kuma ...
written 10.4 years ago by anna freni sterrantino120
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Answer: A: Principal component analysis
... Hello, you can take a look here http://cran.fhcrc.org/ or also help.search("prinicpal components") and ?princomp Cheers Anna Anna Freni Sterrantino Ph.D Student Department of Statistics University of Bologna, Italy via Belle Arti 41, 40124 BO. ________________________________ A: bioco ...
written 10.7 years ago by anna freni sterrantino120
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Answer: A: results.summary does not recognize annotations
... Hi Peter, If I understood what you mean, you may want to try mget(significant, hgu95av2SYMBOL) well of course significant is a vector of characters Best Regards Anna Anna Freni Sterrantino Ph.D Student Department of Statistics University of Bologna, Italy via Belle Arti 41, 40124 BO. ____ ...
written 10.9 years ago by anna freni sterrantino120
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Answer: A: How to carry out Gene Set Enrichment Analysis(GSEA) on an ordered list of Entrez
... I see what you mean, now that you mention the Broad Institute, as long I know, the pre-ranked list of genes is ranked to reflect differential expressions between two classes, and not as in you case just by fold change values. Any way form Bioconductor, if you know at least the chip form where yo ...
written 11.2 years ago by anna freni sterrantino120
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How to carry out Gene Set Enrichment Analysis(GSEA) on an ordered list of Entrezgene ids?
... Hi Chanchal , as long you have only a list on entrezID, there is not much to do, oh well: Of course you can get gene sets ,information related to the gene set structure, description etc it should be fine, with GSEABase. But to perform a Gene Set Enrichment Analysis, ( in a more general framewor ...
proteomics hgu95av2 gseabase written 11.2 years ago by anna freni sterrantino120

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