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User: lynski008

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lynski0080
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Posts by lynski008

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Comment: C: Error when calculating DE using the classical approach in edgeR
... Many thanks for your helpful suggestions.  I am now calculating differential expression using the GLM approach.  One further question: you say that supplying design to estimateDisp will use the GLM approach for estimating the dispersions.  Does this mean that I don't need to go back and use qlmQLFit ...
written 2.5 years ago by lynski0080
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Error when calculating DE using the classical approach in edgeR
... I am trying to use edgeR to analyse differential gene expression from my RNA-seq dataset.  The experimental design is as follows: I had 3 different treatment conditions i.e. 1 factor with 3 different levels.  And there are 3 replicate RNA samples (counts libraries) for each of the 3 treatments i.e. ...
edger differential expression rna-seq written 2.5 years ago by lynski0080 • updated 2.5 years ago by Gordon Smyth36k
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Comment: C: edgeR filtering: how to remove meta tags and lowly expressed reads (cpm)
... That worked perfectly.  Thank you very much Gordon. ...
written 2.5 years ago by lynski0080
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edgeR filtering: how to remove meta tags and lowly expressed reads (cpm)
... I'm attempting to use edgeR to analyse my RNA-seq data.  I have managed to use readDGE to create a data object which I have called DG and it looks like this if I print it:  An object of class DGEList $samples files group lib.size norm.factors counts3D7_1-1 counts3D7_1-1 1 ...
edger filtering cpm written 2.5 years ago by lynski0080 • updated 2.5 years ago by Gordon Smyth36k

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