User: colaneri

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colaneri30
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United States
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6 months, 3 weeks ago
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2 years, 6 months ago
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Posts by colaneri

<prev • 21 results • page 1 of 3 • next >
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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 7 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 8 months ago by colaneri30 • updated 8 months ago by James W. MacDonald45k
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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 8 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 8 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 8 months ago by colaneri30 • updated 7 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 8 months ago by colaneri30
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Comment: C: Missing GenBank accession numbers in the org.Hs.egACCNUM object?
... I see, thanks for the clarification. Then I guess the question is: is there any available tool to convert this accnum to gene identifiers. Because those accnum I am having problem to convert comes from papers reporting gene expression differences measured by micro array. That means that they were u ...
written 8 months ago by colaneri30
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Missing GenBank accession numbers in the org.Hs.egACCNUM object?
... I am trying to convert GenBank accession numbers to Entrez ID or Symbol using the org.Hs.egACCNUM object. However many of the GenBank accnum in my list do not exist in the object. The description of this object says: “This object is a simple mapping of Entrez Gene identifiers https://www.ncbi.nlm.ni ...
bioconductor org.hs.eg.db written 8 months ago by colaneri30 • updated 8 months ago by James W. MacDonald45k
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Comment: C: DESeq2, Still a most genes get padj=NA after declare cooksCutoff=FALSE in the re
... Dear Michael, according to the vignette the automatic independent filtering is setting the adjusted p values to NA because it considerer that those genes have a low mean normalized count. I found that only 1600 genes were considered to have a good number of counts. When I look at the data I found th ...
written 19 months ago by colaneri30
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DESeq2, Still a most genes get padj=NA after declare cooksCutoff=FALSE in the results () function
... Hi Im doing DGE analysis with DESeq2 to test difference in gene expression under 2 conditions. As other people reported in this foro I got a bunch of genes with NA. However in my case the NA value is in their majority for padj. (see table below) In other words I have a bunch of genes with very low p ...
deseq2 na cookscutoff written 20 months ago by colaneri30 • updated 20 months ago by Michael Love14k

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