User: Friederike

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Friederike10
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Location:
NUC, Weill Cornell Medicine
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6 months, 4 weeks ago
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7 months, 1 week ago
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f******@med.cornell.edu

Posts by Friederike

<prev • 6 results • page 1 of 1 • next >
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Comment: C: Why does scran's computeSumFactors produce different size factors for cells with
... sorry, just saw this now. alright, so let's see if I get this right: I should try to find cells that have inconspicuous counts, but low gene numbers. In the example posted today, I excluded cells with less than 500 genes, so I thought I was on the somewhat safe side. Let me check what's going on in ...
written 7 months ago by Friederike10
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Comment: C: Why does scran's computeSumFactors produce different size factors for cells with
... alright. here's the problem: the extreme values do not stem from contaminations. they are, indeed, the marker gene(s) of these particular cells. ...
written 7 months ago by Friederike10
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Comment: C: Why does scran's computeSumFactors produce different size factors for cells with
... thanks, will look into that! PS: I was loosely following your workflow - there you specifically just check for the lower tail when excluding cells based on library size and gene counts, so I didn't pay enough attention to the other end of the spectrum, I guess ...
written 7 months ago by Friederike10
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Comment: C: Why does scran's computeSumFactors produce different size factors for cells with
... Ok, so here's what happened with more stringent filtering of cells (at least 500 genes per cell) - I'll post the code to make sure that it's not just all due to me setting a wrong parameter. # 1. filtering cells > mito.drop <- sceset$pct_counts_feature_controls_mito >= 50 | is.na(sceset$p ...
written 7 months ago by Friederike10
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Comment: C: Why does scran's computeSumFactors produce different size factors for cells with
... Hi Aaron, thanks for the quick reply! * What would you consider "low read count"? With a different data set I tend to follow Seurat's default of min. 500 genes per cell, but this particular data set we wanted to explore rare cell types which is why I've been trying to keep the filtering to a minim ...
written 7 months ago by Friederike10
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Why does scran's computeSumFactors produce different size factors for cells with the exact same gene counts?
... Hi, I've been playing around with different normalization strategies for scRNA-seq data. Contrary to the header, I think, I have actually two questions, the first one being: Is the computeSumFactors() philosophy really applicable to current Drop-seq data sets? The sample that initiated the questio ...
scran scater scrnaseq drop-seq written 7 months ago by Friederike10 • updated 7 months ago by Aaron Lun17k

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