User: baus87

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baus870
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Posts by baus87

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Comment: C: edgeR - MDS Plot for Count Data
... Aaron, it is necessary to do low counts filtering before voomWithQualityWeights? ...
written 10 weeks 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 10 weeks 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 11 weeks 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 12 weeks 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 3 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 3 months ago by baus870
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Comment: C: edgeR - MDS Plot for Count Data
... Dear Aaron, i've just run voomWithQualityWeights. The "counts" argument was a DGEList object and normalization factors were previously calculated by calcNormFactors(DGEList object). This is the output: << An object of class "EList" $targets    group lib.size norm.factors C1     C 25314293     ...
written 3 months ago by baus870
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edgeR - MDS Plot for Count Data
... Hello there,  i'm doing a DEGs analysis based on RNA-seq data. I've got 2 experimental thesis and 3 biological replicates each. Here is attached the relative MDS plot for count data and i was wandering if it is a good idea to do not take into account replicate "C1" for downstream analysis or, howeve ...
edger plot mds deg written 3 months ago by baus870
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Common dispersion value using edgeR for DEGs analysis
... Dear all, i'm doing a DEGs analysis on edgeR.  Count reads are from a RNA-seq experiment based on 2 thesis and 3 bio. rep.s each. We're talking about 10k genes odd. (so the generated matrix is a 6, columns, per 10k, raws) The common dispersion value is 0.04. Could it be considered a good value? Co ...
edger degs common disperion written 3 months ago by baus870 • updated 3 months ago by Aaron Lun17k

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