User: Aurora

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Aurora10
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1 month ago
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5 months, 2 weeks ago
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Posts by Aurora

<prev • 25 results • page 1 of 3 • next >
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Comment: C: constructing a DESeqDataSet
... As far as I understood, DESeqDataSetFromTximport has the same purpose that DESeqDataSetFromMatrix but it can directly accept the output of a psedoaligner such as Salmon, producing directly the count matrix. With DESeqDataSetFromMatrix, you need to have a count matrix already prepared with genes as ...
written 11 weeks ago by Aurora10
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What does the relative-log expression normalization mean in the deseq2 wrapper function ?
... Good morning, I am trying to understand the relative log expression normalizat ion made by the DESEQ2 wrapper function. As far as I understood, It corresponds to the computing of scaling factor as described by Anders and Hubers (https://genomebiology.biomedcentral.com/articles/10.1186/gb-2010-11- ...
normalization deseq2 rle written 11 weeks ago by Aurora10 • updated 11 weeks ago by Michael Love19k
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Pathview results interpretation
... Good morning ! I have kegg pathway modification results thanks to pathview but I don't know how to interpret it. A rectangle corresponds to a gene ? A rectangle can be both green and red, what does it mean according to its regulation ? Why does the lengend values always go from -1 to 1 ? How can I ...
pathview interpretation written 11 weeks ago by Aurora10
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Comment: C: Troubles installing GO.db
... Thanks a lot ! I didn't notice that detail on this new computer. ...
written 11 weeks ago by Aurora10
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Troubles installing GO.db
... Good morning, I can"t install the GO.db package and I can't figure out how to do it. > biocLite("GO.db") BioC_mirror: https://bioconductor.org Using Bioconductor 3.7 (BiocInstaller 1.30.0), R 3.5.0 (2018-04-23). Installing package(s) ‘GO.db’ installing the source package ‘GO.db’ trying URL 'h ...
go.db written 11 weeks ago by Aurora10 • updated 11 weeks ago by Martin Morgan ♦♦ 22k
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GAGE function and the same.dir option
... Good morning, I am trying to find perturbed pathway from expression date using a kegg gene set. In the GAGE paper (Luo et al., 2009), iit is recommanded to use the option same.dir=F on KEGG pathwayt is worthy to run gage with  to capture pathways perturbed towards both directions simultaneously. ...
gage gene set testing written 11 weeks ago by Aurora10 • updated 11 weeks ago by Luo Weijun1.4k
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Comment: C: Filtering Rna-seq counts
... Thanks a lot ! ...
written 12 weeks ago by Aurora10
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Filtering Rna-seq counts
... Hi, Filtering Rna-seq counts before performing differential expression analysis is generally recommanded. I wonder why is it recommanded?  What makes the analysis better that if no filtering was performed.?   Thank you for answers   ...
rna-seq filtering written 12 weeks ago by Aurora10 • updated 12 weeks ago by Gordon Smyth34k
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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 3 months ago by Aurora10 • updated 3 months ago by Gordon Smyth34k
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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 3 months ago by Aurora10

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