User: bkleiboeker

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bkleiboeker20
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Posts by bkleiboeker

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Comment: C: Am I unnecessarily 'missing' a high number of true-positive DE genes? Or do I ju
... I never knew of that function, thank you for that! When I run that on my filtered data, I get the following: > propTrueNull(qlf$table$PValue) [1] 0.7799189 Does this mean that 77% of my total genes (n=14,000) are truly not DE, or that 77% of my genes with p less than some cutoff are in reality ...
written 4 days ago by bkleiboeker20
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Comment: C: Am I unnecessarily 'missing' a high number of true-positive DE genes? Or do I ju
... That's great to hear, thank you! ...
written 4 days ago by bkleiboeker20
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Comment: C: Am I unnecessarily 'missing' a high number of true-positive DE genes? Or do I ju
... I have also experimented with the `filterByExpr()` function but was unaware that it automated this process. Does it automate when you don't pass in any arguments for `min.count` and `min.total.count`? Because I had always been supplying my own values for those two parameters. Thank you for your resp ...
written 4 days ago by bkleiboeker20
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Am I unnecessarily 'missing' a high number of true-positive DE genes? Or do I just not understand the statistics?
... Hi all, I am doing a RNAseq analysis for DE genes. In my initial analysis, using the arbitrary cutoff of 1 CPM for filtering out lowly expressed genes, I found ~20 DE genes (i.e. genes with FDR = p.adjust(method="BH") < 0.05). I have been working to understand the BH correction, and in my explor ...
R rna-seq edger written 4 days ago by bkleiboeker20 • updated 4 days ago by _r_am32k
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Answer: A: Matching gene ids in R
... Here's an workaround I use sometimes to extract a column from one df to another by aligning one row, like geneIDs: Say column 2 in df1 contains logCPM values, then we could 'collect' those values in a new column in df2 (call it df2$logCPM) by like geneID using df2$logCPM<-as.matrix(df1)[,2] ...
written 15 days ago by bkleiboeker20
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Answer: A: How to add gene names to DGEList and convert to csv? gro-seq groHMM
... Will answer in case someone stumbles upon this in the future: #for your DGElist, kgLimit counts <- as.data.frame(kgLimit$counts) row.names(counts) <- kgLimit$symbol #this may need to be as.vector(kgLimit$symbol), I'm not good enough with R to know off the top of my head ...
written 16 days ago by bkleiboeker20

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