User: baus87

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baus870
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Posts by baus87

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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 2 days 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 2 days 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 days 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 days ago by baus870 • updated 4 days ago by Gordon Smyth32k
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Comment: C: edgeR - MDS Plot for Count Data
... Aaron, it is necessary to do low counts filtering before voomWithQualityWeights? ...
written 5 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 5 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 5 months ago by baus870
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Answer: A: edgeR - MDS Plot for Count Data
... Dear Aaron, i've performed a gene ontology analysis on DEGs found in C1 replicate. The biological functions of these DEGs are wired to the following roles: DNA modification (especially that involving in DNA repair), regulation of transcription/translation, cellular division, protein catabolism, sign ...
written 5 months ago by baus870
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Answer: A: edgeR - MDS Plot for Count Data
... Aaron, as you suggested, i've performed an exactTest on C1vsC2 and C1vsC3 (using the BCV value from the **DEGs analysis in which i took into account all the data set, that's 3 replicates for both the "C" and the "T" condition). After merging together DEGs from C1vsC2 and C1vsC3 analysis, the 7% of t ...
written 6 months ago by baus870
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Comment: C: edgeR - MDS Plot for Count Data
... Dear Aaron, once assumed C1 data are more dispersed than other libraries i investigated raw counts per library. In particular, i've calculated the pairwise correlation among C1, C2, C3 in three distinct groups, that is: (i) differential expressed genes (ii) non-differential expressed genes and (iii) ...
written 6 months ago by baus870

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