User: Asta Laiho

gravatar for Asta Laiho
Asta Laiho120
Reputation:
120
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Location:
Finland
Last seen:
3 years, 9 months ago
Joined:
9 years, 1 month ago
Email:
a*********@utu.fi

Posts by Asta Laiho

<prev • 17 results • page 1 of 2 • next >
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Problem in KEGGREST package function keggConv
... Hi, I'm trying to convert uniprot identifiers to KEGG identifiers using KEGGREST:keggConv but suddenly this has stopped working (I'm doing this routinely). I tried with many common genes and it returns an empty string (examples below). Does anyone know why this might be? >  keggConv("hsa", "uni ...
keggrest keggconv written 3.8 years ago by Asta Laiho120 • updated 3.8 years ago by Dan Tenenbaum8.2k
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RamiGO: getAmigoTree producing internal server errors
...     Hi,     I have been using RamiGO for producing GO graphs for quite a while but recently it has started crashing with internal server errors. The problem seems to be related to certain GO terms (many of them actually).   List of goIDs and associate pvalues:   > goIDs   [1] "GO:0003735 ...
ramigo written 4.5 years ago by Asta Laiho120
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Answer: A: Gviz::plotTracks for BiomartGeneRegionTrack() produces empty plots
... Many thanks - it works perfectly now! :) ...
written 4.8 years ago by Asta Laiho120
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Answer: A: Gviz::plotTracks for BiomartGeneRegionTrack() produces empty plots
... Hi Florian, Thanks for the advice, this way it indeed seems to work for hg19. I would also need to produce plots for mm10 and I still get only empty plots even after trying:  bm <- useMart(host="feb2014.archive.ensembl.org",biomart="ENSEMBL_MART_ENSEMBL",dataset="mmusculus_gene_ensembl")   fm & ...
written 4.8 years ago by Asta Laiho120
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Gviz::plotTracks for BiomartGeneRegionTrack() produces empty plots
...   Hi, I’m trying to plot gene models in a specific region using Gviz package and BiomartGeneRegionTrack function. I have tried with different regions and genomes (one below as an example) but the returned plot is always empty although the regions should contain annotated Ensemble genes. When I plo ...
visualization gviz written 4.8 years ago by Asta Laiho120
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RamiGO package function getAmigoTree broken
... Hi, I have routinely used the RamiGO package (that I really like!) for plotting go graphs but now something seems to have gone broken for the getAmigoTree function: goIDs <- c("GO:0051130","GO:0019912","GO:0005783") color <- c("lightblue","red","yellow") pp <- getAmigoTree(goIDs=goIDs,col ...
go ramigo written 5.6 years ago by Asta Laiho120 • updated 5.6 years ago by Dan Tenenbaum8.2k
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Reactome support for more organisms
... Hi, It seems to me the reactome.db package is based on human content of the Reactome database (Entrez identifiers, mappings to GO, etc). I would be delighted to see support added for other organisms (especially for mouse) as Reactome database anyhow supports them. Any plans for that yet? - Asta ...
go written 6.5 years ago by Asta Laiho120 • updated 6.5 years ago by Marc Carlson7.2k
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Problem in KEGGSOAP package
... Hi, There seems to be some problem in the KEGGSOAP package: > library(KEGGSOAP) failed to load HTTP resource Error : .onLoad failed in loadNamespace() for 'KEGGSOAP', details: call: NULL error: 1: failed to load HTTP resource Error: package/namespace load failed for ?KEGGSOAP? I wonder i ...
keggsoap written 6.8 years ago by Asta Laiho120 • updated 6.8 years ago by Dan Tenenbaum8.2k
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Comment: C: cummeRbund package function diffData returns no rows for TSS features
... Hi, After importing the reshape the database is succesfully rebuilt: cuff CuffSet instance with: 4 samples 22260 genes 37557 isoforms 27776 TSS 25411 CDS 133002 promoters 166656 splicing 101436 relCDS However, the diffData for ...
written 7.7 years ago by Asta Laiho120
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cummeRbund package function diffData returns no rows for TSS features
... Many thanks for a quick response! I installed the version 1.1.3 and tried rebuilding the database but got the following error: cuff <- readCufflinks(rebuild=T) Creating database /Users/alaiho/Documents/Data-analysis/Projects/NGS/1 10007_Liisa_Nissinen/cufflinks/cuffdiff_output/cuffData.db Readi ...
rnaseq cummerbund written 7.7 years ago by Asta Laiho120 • updated 7.7 years ago by Loyal Goff140

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Popular Question 3.8 years ago, created a question with more than 1,000 views. For gsea (gene set enrichment analysis) for ranked lists

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