User: prat

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prat0
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Posts by prat

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FNR in RNASeq
... Why are false neg rates usually not seen/used for RNASeq analysis? My guess is that the TP is not known... Is it possible to still calculate/estimate the FNR in DESeq2/edgeR? ...
edger deseq2 written 7 weeks ago by prat0 • updated 7 weeks ago by Gordon Smyth38k
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DESeq2 v1.16 more than two conditions
... How are multiple conditions/comparisons done in v1.16 using lfcShrink?  Using the example from the package, eg. cnts <- matrix(rnbinom(n=1500, mu=100, size=1/0.5), ncol=15) cond <- factor(rep(1:3, each=5)) # object construction dds <- DESeqDataSetFromMatrix(cnts, DataFrame(cond), ~ cond) ...
deseq2 written 20 months ago by prat0 • updated 20 months ago by Michael Love24k
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Design matrix not of full rank
... My design matrix is below for an RNASeq experiment and somewhat similar to Section 3.4.2 Blocking in the manual I'm trying to follow, sample    condition    mouse ctrl_minus_1    ctrl_minus    1 ctrl_plus_1    ctrl_plus    1 ko_minus_1    ko_minus    2 ko_plus_1    ko_plus    2 ctrl_minus_2    ctrl ...
edger written 3.4 years ago by prat0 • updated 3.4 years ago by Aaron Lun24k

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Popular Question 20 months ago, created a question with more than 1,000 views. For Design matrix not of full rank

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