User: Aurora

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Aurora10
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11 months, 2 weeks ago
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1 year, 7 months ago
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Posts by Aurora

<prev • 27 results • page 2 of 3 • next >
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Where is it possible to find gene sets in rdata format for GSEA ?
... I would like to perform GSEA in R using the camera method from limma. However I work on Rattus Norvegicus data and I don't find any Rdata file available to use as a gene set. I only foud this website : http://bioinf.wehi.edu.au/software/MSigDB/mouse_c2_v5p1.rdata but gene sets are only available for ...
rattus norvegicus gsea written 18 months ago by Aurora10 • updated 18 months ago by Gordon Smyth39k
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Noiseqbio function (NOISEQ package)
... Hi, I am trying to use the Noiseqbio method in order to compare the results with other methods (edger, deseq2 and limma+voom). I obtain very similar results for edger, deseq2 and limma+voom but i obtain completely different results (twices more DE genes) when i use noiseqbio. I think i did not us ...
noiseq logfoldchange written 18 months ago by Aurora10
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Comment: C: How does the function model.matrix (to define experimental design) really works
... Thanks a lot for this explanation !  ...
written 19 months ago by Aurora10
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How does the function model.matrix (to define experimental design) really works ?
... Good morning, I am working with edgeR to perform differential expression on rna-seq data. I have a design with two variables :  type (obese/normal) and treatment type is a vector with two levels (obese/normal) treatment is a vector with 5 levels ( 5 different treatments) But when I perform this ...
edger experimental design model.matrix written 19 months ago by Aurora10 • updated 19 months ago by Ryan C. Thompson7.4k
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How to compare RNA-seq counts matrices from different aligners ?
... I have used an aligner to produce raw counts from a publicRNA-seq data (GSE63310 , the counts are available online). I would like to compare my results with the "official ones" on the GEO website but I don't know how to compare accurately these two matrices to have an idea of their similarity. Than ...
rnaseq counts alignement written 19 months ago by Aurora10
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Comment: C: Biomart error message
... These commands seem to work :   > require(biomaRt) > human = useMart("ensembl", dataset = "hsapiens_gene_ensembl",                  +                 host = "http://Aug2017.archive.ensembl.org&quot;, +                 verbose = TRUE) Attempting web service request: http://Aug2017.ar ...
written 19 months ago by Aurora10
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Answer: A: Biomart error message
... ty for answer , I see this if I go to http://Aug2017.archive.ensembl.org:80/biomart/martservice?type=registry&requestid=biomaRt : <MartRegistry> <MartURLLocation database="ensembl_mart_90" default="1" displayName="Ensembl Genes 90" host="aug2017.archive.ensembl.org" includeDatasets ...
written 19 months ago by Aurora10
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Biomart error message
... Good Morning,  I am trying to use Biomart to annotate genes but I always have this error message that appears :  The query to the BioMart webservice returned an invalid result: biomaRt expected a character string of length 1. Please report this to the mailing list. I find a subject on bioconducto ...
biomart written 19 months ago by Aurora10
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Comment: C: results {DESeq2} parameters
... Ok thanks a lot ! So when you wannt only genes with a log FC between two conditions to be greate in absolute value than a threshold is it better to use the lfc Threshold parameter in the results function or is it ok if it's set to 0 by default ? thanks a lot,  have a good day ...
written 19 months ago by Aurora10
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Comment: C: results {DESeq2} parameters
... i already read the details about these two arguments, but I didn't understood. For lfcThreshold is is writen :" a non-negative value which specifies a log2 fold change threshold." so I understood it as a threshold filter as well for alpha "the significance cutoff used for optimizing the independent ...
written 19 months ago by Aurora10

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