User: colaneri

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colaneri30
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United States
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7 months, 3 weeks ago
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3 years, 5 months ago
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Posts by colaneri

<prev • 25 results • page 1 of 3 • next >
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Answer: A: How to produce a dataframe with unique ENTREZID to use in gage?
... Right & thank for the clarification! I am still trying to produce a dataframe with uniquely mapped pairs of IDs (e.g  ENSEMBL -> ENTREZID or SYMBOL -> ENTREZID) Can you tell me why such a different results using two different databases? and which one you will use to go to gage-pathview? ...
written 7 months ago by colaneri30
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How to produce a dataframe with unique ENTREZID to use in gage?
... Hi I have a dataframe of reads-counts (CNTS) with 47,540 unique ENSEMBL IDs. Now I want to use gage to test for differences in gene expression over gene-sets (e.g KEGG pathways) For example: SIG.keeg.p <- gage(CNTS, gsets=kegg.sig, ref= ref.idx, samp = samp.idx, compare = "as.group") To use ga ...
annotationdbi gage ensembl entrez written 7 months ago by colaneri30
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Answer: A: Error when installing package gageData
... Dear Luo Thanks for the answer, I have also noticed what you are saying but unfortunately that is what got after running the installation of gageData this is what I got once I run: biocLite("gageData") I did install other packages (like gage in self) today and I have not problem. Any idea?     ...
written 8 months ago by colaneri30
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Error when installing package gageData
... Hi I am trying to install the gage data package from bioconductor:   source("https://bioconductor.org/biocLite.R") biocLite("gageData") However I got this error during installation (see below). I have not idea how to solve this problem. Any suggestion? ALe ##################################### ...
gage kegg written 8 months ago by colaneri30
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How to update the list of genes mapped to GO terms in the topGO object?
... I understand that the annFUN function compiles the GO terms and map genes to those terms. However when I checked the number of genes annotated for a particular GO term in my topGO object, and I compared it  with the AMIGO2 database, I noticed a big difference. For example GO:0045665 have 82 genes i ...
go topgo written 18 months ago by colaneri30
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Error when using the showGroupDensity function in topGO
... I like to study the distribution of the genes annotated to a GO term of interest. One that is significant enriched in my topGO analysis and for that i use the showGroupDensity function. But I get the following error: print(showGroupDensity(GOdataUP, goID, ranks = F)) Error in print(showGroupDensit ...
topgo written 19 months ago by colaneri30 • updated 19 months ago by James W. MacDonald48k
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topGO plotting options: It is possible to control the number of nodes in the DAG plot according with their p values?
... Dear all. The firstSigNodes argument in the function that plots DAG in topGO allows to control the number of "TOP ranked" significant GO terms that will be including in the DAG. However the problem is that parents GO terms are also included in  the final DAG. That fill the plot with nodes that do n ...
topgo dag written 19 months ago by colaneri30
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Comment: C: goseq Error: could not find function "supportedOrganisms"
... James, sorry but I do not follow why updating to the current version of R will help. The package I am having problem with is older than this R 3.3.3 version and it should be working fine with my R version 3.2.2.  I check for the version you suggested at it looks is really new News R version 3.3.3 ...
written 19 months ago by colaneri30
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goseq Error: could not find function "supportedOrganisms"
... I installed goseq and when I call: SO <- supportedOrganisms() Error: could not find function "supportedOrganisms" supportedGenomes() Error in getNodeSet(doc, "//table[@class='descTbl']")[[1L]] : subscript out of bounds A Similar question have been posted here:  https://support.bioconductor ...
goseq written 19 months ago by colaneri30 • updated 18 months ago by edmund.wright0
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Problem when using topGO for RNAseq data: The number of annotated genes for GO terms changes according to the number of genes in the gene-background-LIst.
... I’am running topGO, to perform GO analysis in a RNA-seq data set. I have an small data set of 104 significant genes that I called “sigG”. Firstly, I used genefilter to find genes that have similar level of expression than my “sigG”.  For each sigGene I got 10 genes which make a background set of 10 ...
rnaseq topgo gene ontolology written 19 months ago by colaneri30

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Popular Question 17 months ago, created a question with more than 1,000 views. For Error: could not find function "rlog"
Popular Question 17 months ago, created a question with more than 1,000 views. For How to install S4Vector package in R v 3.1.1?

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