User: baus87

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baus870
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Posts by baus87

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Comment: C: Limma - how to manage huge differences in library sizes
... Dear Gordon, the situation in my experiment was actually the opposite: the "treatment" condition is full of genes having 0 counts in all libraries (4). In such situation, by using voom with quality weights, I got some up-regulated genes (contrast matrix: T-C) having 0 counts in all libraries.  Howe ...
written 5 weeks ago by baus870
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Comment: A: Limma - how to manage huge differences in library sizes
... Dear Wolfgang, thanks for your reply. Actually it's a consequence of experimental design. We're talking about fungal pure culture (control condition) vs. an in planta fungal interaction at the very early stage of fungal growth. Regrettably, we do not have negative control. Also, the failure in prop ...
written 5 weeks ago by baus870
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Limma - how to manage huge differences in library sizes
... Dear Bioconductor community, i'm performing a differential expression analysis (classic approach: treatment vs control condition) in which library sizes of biological replicates of control thesis exceed of 100 times those of treatment condition. The software used, limma, is impaired in DEGs detecti ...
limma written 5 weeks ago by baus870 • updated 5 weeks ago by Gordon Smyth33k
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Comment: C: How to create a customized OrgDb in order to perform kegga analysis?
... Dear Guido, nowadays i'm annotating my reference genomes with ko codes from KEGG. Given a set o differentially expressed genes, I was just looking for the proper enrichment analysis to be applied. Maybe my first post has been misleading, sorry for that. Antonio ...
written 3 months ago by baus870
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Comment: C: How to create a customized OrgDb in order to perform kegga analysis?
... Ok, got it. Could you recommend me any alternative tool? ...
written 3 months ago by baus870
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Comment: C: How to create a customized OrgDb in order to perform kegga analysis?
... Dear Gordon, i'm working with Trichoderma gamsii (filamentous fungus). I'd like to perform a kegg enrichment analysis upon DEGs. Is it kegga suitable for this purpose? ...
written 3 months ago by baus870
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How to create a customized OrgDb in order to perform kegga analysis?
... Hi, i'm working on a set of DEGs and i'd like to analyze them using the kegga function. Since i'm working on a species whose OrgDb is not implemented in, how can i create an in-house dedicated OrgDb? thanks in advance, Antonio ...
orgdb limma kegga written 4 months ago by baus870 • updated 4 months ago by Gordon Smyth33k
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Comment: C: edgeR - MDS Plot for Count Data
... Aaron, it is necessary to do low counts filtering before voomWithQualityWeights? ...
written 9 months ago by baus870
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Comment: C: edgeR - MDS Plot for Count Data
... This is what came up after performing voomWithQualityWeights and estimateCommonDisp: > edgeRobject <- voomWithQualityWeights(edgeRobject, design=NULL, lib.size=NULL, normalize.method="none",plot=FALSE, span=0.5, var.design=NULL, method="genebygene", maxiter=50, tol=1e-10, trace=FALSE, col=NU ...
written 9 months ago by baus870
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Comment: C: edgeR - MDS Plot for Count Data
... Dear Aaron, how to deal with negative logCPM after performing voomWithQualityWeights in order to calculate dispersion? ...
written 9 months ago by baus870

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