User: Zach Roe

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Zach Roe10
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Posts by Zach Roe

<prev • 14 results • page 1 of 2 • next >
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Comment: C: DESeq2: Difference in rlog and vst values if run transform before or after runni
... Hi Michael I am still trying to figure out where the discrepancy occurs.  I had also been filtering using fpm and thought that was causing the error but I cannot reproduce the error when using the example DESeqDataSet. ...
written 2.7 years ago by Zach Roe10
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DESeq2: Difference in rlog and vst values if run transform before or after running DESeq
... Hi, I notice that the rlog and vst values for my assay differ depending if I run the DESeq function before or after running the transformation. I thought that did this not matter as the manual states under section Data transformations and visualization -- "However, the running times are shorter an ...
deseq deseq2 rlog variancestabilizingtransformation written 2.7 years ago by Zach Roe10 • updated 2.7 years ago by Michael Love26k
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Comment: C: dendextend: color_branches not working for certain hclust methods
... Apologies, I just realize dendextend is not a Bioconductor package, I cross-posted on stack overflow: https://stackoverflow.com/questions/42406763/r-dendextend-color-branches-not-working-for-certain-hclust-methods ...
written 2.7 years ago by Zach Roe10
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dendextend: color_branches not working for certain hclust methods
... Hi, I am using dendextend to plot hclust tree objects generated by each hclust method from hclust{stats}: "ward.D", "ward.D2", "single", "complete", "average" (= UPGMA), "mcquitty" (= WPGMA), "median" (= WPGMC) or "centroid" (= UPGMC). I notice the color coding for color_branches fails when I use ...
dendextend written 2.7 years ago by Zach Roe10
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Comment: C: DESeq2: Applying different pre-filtering for DE and EDA/Visualization of RNASeq
... Hi Michael, I went with this solution and have follow up questions. 1. I see there is no dds$baseMean, I assume you mean res$baseMean, my code so far, setting alpha=0.05 which is the FDR cutoff I want to use downstream: res1 <- results(dds, contrast=c("condition", group1, group2), alpha=0.05) ...
written 2.7 years ago by Zach Roe10
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Comment: C: DESeq2 cooksCutoff ON/OFF: pairwise contrasts for many groups, some with only 2
... Sorry for my confusion, thank you for pointing that out.  Then I should apply any filtering criteria before controlling for FDR and not after? Roez  ...
written 2.8 years ago by Zach Roe10
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Comment: C: DESeq2 cooksCutoff ON/OFF: pairwise contrasts for many groups, some with only 2
... Thank you Michael.  I am wondering if I could run all the contrasts as is (ignoring the non-flagging in the 2 sample cases), set my adj. p-val and lfc cut off, but after this DE analysis set a criteria that filters the DE genes further... possibly using the mean vs. difference pairwise-plots of all ...
written 2.8 years ago by Zach Roe10
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Comment: C: DESeq2: Applying different pre-filtering for DE and EDA/Visualization of RNASeq
... Thank you Michael. I was planning to use the same common filter across the different contrasts, and I really like this suggestion so that I don't have to make an arbitrary decision for cutoff. Can I ask for clarification: I initially run all contrasts with no pre-filtering correct? And then impleme ...
written 2.8 years ago by Zach Roe10
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Comment: C: DESeq2: Applying different pre-filtering for DE and EDA/Visualization of RNASeq
... Thank you Ryan, I have not used edgeR before only DESeq2, can I ask clarification in terms of the down-weighting of the contribution of low count genes is that specific to application for clustering and PCA only?  I like the idea of not excluding them outright and will read through the implementatio ...
written 2.8 years ago by Zach Roe10
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DESeq2: Applying different pre-filtering for DE and EDA/Visualization of RNASeq data
... Hello,  I am searching for advice regarding choosing the level of pre-filtering before using DESeq differential expression, and pros/cons or acceptability of applying different pre-filtering levels for DE vs downstream analysis involving count transformation for EDA/visualization including hierarch ...
deseq2 pre-filtering written 2.8 years ago by Zach Roe10 • updated 2.8 years ago by Michael Love26k

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