User: knaxerova

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knaxerova10
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Posts by knaxerova

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Comment: C: EdgeR analysis of bottlenecked genetic screen data
... Haha. And you’re like: not useless at all, only precise! Totally understood and agreed about the proportions. One has to be comfortable with that scientific question. For the particular experiment I am analyzing it is actually appropriate, as cells are separated into two pools by FACS that are then ...
written 19 days ago by knaxerova10
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Comment: C: EdgeR analysis of bottlenecked genetic screen data
... Well, fortunately I have a number of positive controls in the experiment, and they are correctly appearing at or near the very top of the list, so I have a measure of correctness in that regard. It therefore seems to me that edgeR is doing a good job handling these data overall. Many screens in whic ...
written 20 days ago by knaxerova10
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Comment: C: EdgeR analysis of bottlenecked genetic screen data
... Thanks Aaron. * Counts are gRNAs in a genome-wide screen. * The features I listed were just for illustrative purposes. The actual dataset would have tens of thousands of features. * The bottleneck is severe, such that counts for a majority of the genes (or perhaps more like 75%) become 0. * I ch ...
written 20 days ago by knaxerova10
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EdgeR analysis of bottlenecked genetic screen data
... Hi everyone,  I have been analyzing genetic screen data with edgeR for years -- my favorite toolbox! Now I was hoping to get people's opinions about a special case: analysis of bottlenecked data.  Let's say an assay takes a reagent library through some sort of severe bottleneck, such that the resu ...
edger written 20 days ago by knaxerova10 • updated 20 days ago by Aaron Lun20k
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Is there a way to set the ClusterProfiler color gradient?
... Hi everybody,  the color gradient in the newest version of ClusterProfiler (3.8.0) has changed when using dotplot() to visualize a compareClusterResult object. It used to be red->purple and now is red->yellow->blue. Is there a way to change this/set the color scale? The issue is that this ...
clusterprofiler written 8 weeks ago by knaxerova10
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Comment: C: edgeR: Should there be a normalization step for CRISPR screens? How to deal with
... Yes, the comparisons I am doing with edgeR are sorted cells vs. the pool from which they were separated. The main question I have is which guides are differentially enriched in the sorted pool (it’s really impossible to look for dropouts). My current (if not ideal) approach is to create a DGElist ob ...
written 7 months ago by knaxerova10
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Comment: C: edgeR: Should there be a normalization step for CRISPR screens? How to deal with
... Thanks! Regarding the sorted cells, it sounds like what I have already been doing (edgeR with library normalization) is the best approach then, even if it's not ideal... I wonder whether there is a way to identify the potential "errors in scaling normalization" that you are referring to?  With the ...
written 7 months ago by knaxerova10
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Answer: A: edgeR: Should there be a normalization step for CRISPR screens? How to deal with
... Thanks a lot Aaron! I totally agree with you, for small screens TMM may not be suitable, but I think it is a good choice for genome-wide screens. The case studies we discussed (which are also in the edgeR user guide) are genome-wide screens and they don't do it, but I think I will go ahead and do TM ...
written 7 months ago by knaxerova10
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Comment: C: edgeR: Should there be a normalization step for CRISPR screens? How to deal with
... Yes. Specifically the approach shown in section 6. Thanks! ...
written 7 months ago by knaxerova10
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edgeR: Should there be a normalization step for CRISPR screens? How to deal with bottlenecked screens?
... Hi everyone,  I am wondering about the edgeR normalization step (calcNormFactors) for CRISPR screens. The edgeR user guide says that TMM normalization is recommended for RNA-Seq data because "the highly expressed genes can consume a substantial proportion of the total library size, causing the rema ...
edger calcnormfactors written 7 months ago by knaxerova10

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