Question: What information in dispersion plot using edgeR?
1
gravatar for ghmdsr
13 months ago by
ghmdsr30
ghmdsr30 wrote:

I m doing DEG analysis using edgeR.

I have some questions.

  1. Difference between 'edgeR' and 'Limma'
  2. Interpreting 'dispersion plot' : after estimating dispersions

Code:

dgList2 <- estimateGLMCommonDisp(dgList1,design = designMat)
dgList3 <- estimateGLMTrendedDisp(dgList2, design=designMat)
dgList4 <- estimateGLMTagwiseDisp(dgList3, design=designMat)

plotBCV(dgList4)

in this plot, what information can I get? Please help me.

rna-seq tutorial R gene • 826 views
ADD COMMENTlink modified 13 months ago by h.mon26k • written 13 months ago by ghmdsr30

Probably better on the Bioconductor forum.

ADD REPLYlink written 13 months ago by Kevin Blighe45k
1
gravatar for h.mon
13 months ago by
h.mon26k
Brazil
h.mon26k wrote:
  1. edgeR is intended for RNAseq data, and fits a negative binomial model to test for differential gene expression; limma is intended for microarrays, and fits a linear model to test for differential gene expression.

  2. The dispersion is a parameter for the negative binomial model. edgeR uses some fancy techniques to estimate (and possibly squeeze) dispersion from few samples. plotBCV() shows these estimates against the log(counts per million), which is useful for evaluating if the model fit is good and if there is suspicious data lurking in your samples.

ADD COMMENTlink written 13 months ago by h.mon26k

I do feel we need to mention that although limma was originally made for microarrays it continues to be amongst the top tools in benchmarks of DE analysis on RNAseq data - especially when using voom to add weights to the data.

ADD REPLYlink written 13 months ago by kristoffer.vittingseerup2.0k
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