User: rory.kirchner

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Posts by rory.kirchner

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Comment: C: ZINB-WaVE + DESeq2 misses low-expressed, single-condition genes that look like t
... Thanks everyone for the awesome discussion. I put up a github repository here (https://github.com/roryk/zinbwave-deseq2-indrop) that has an rmarkdown report summarizing all of this. In the report are links to the raw data, I put up Seurat object I started with, and a script to calculate the weights ...
written 8 months ago by rory.kirchner60
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Comment: C: ZINB-WaVE + DESeq2 misses low-expressed, single-condition genes that look like t
... Thanks-- I'm an idiot, I was grabbing from the weighted dds object when doing the test instead of the one I created from just the counts. You're right that DESeq2 without the ZINB-WaVE weights catches most of these.   ddsraw = DESeqDataSet(se, design=~1+genoregion) group0NW = ddsraw[, rownames(sub ...
written 8 months ago by rory.kirchner60
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Comment: C: ZINB-WaVE + DESeq2 misses low-expressed, single-condition genes that look like t
... row-wise Wilcoxon does get most of these but only if I grab all the high LFC change genes with the baseMean cutoff in order to not lose them during multiple hypothesis testing correction. True here is padj < 0.05, using BH correction. ...
written 8 months ago by rory.kirchner60
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Comment: C: ZINB-WaVE + DESeq2 misses low-expressed, single-condition genes that look like t
... Hi everyone, to answer everyone's questions: I ran ZINB-WaVE with all ~1700 cells in the experiment, and then subset down to a group I was interested in to do DE across conditions within the different subgroups. I fit it like this: design = model.matrix(~1+genoregion, data=colData(se)) epsilon_de ...
written 8 months ago by rory.kirchner60
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ZINB-WaVE + DESeq2 misses low-expressed, single-condition genes that look like they should be markers
... Hey all, We've been running ZINB-WaVE and DESeq2 on an inDrop dataset to look for differentially expressed genes across subsets of cells. This does a nice job for genes that are more highly expressed, but it looks like this can miss genes that look like they are markers but are expressed at a low l ...
deseq2 differential expression rna-seq single cell zinb-wave written 8 months ago by rory.kirchner60 • updated 8 months ago by Michael Love23k

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