User: knaxerova

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knaxerova10
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United States
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5 days, 23 hours ago
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3 years, 1 month ago
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Posts by knaxerova

<prev • 18 results • page 1 of 2 • next >
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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 6 days 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 5 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 6 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 6 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 6 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 6 months ago by knaxerova10
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Answer: A: CRISPR/RNAi screen time course analysis
... Hi Aaron, thank you for this great answer. I will try out Simes' method. You are pointing out a real concern with the false positives: that is something I am worried about, I will have to see what the results look like in the end. If only one guide out of 5 or 10 scores, it's a bit of a red flag. M ...
written 11 months ago by knaxerova10
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CRISPR/RNAi screen time course analysis
... Hi everyone,  I regularly analyze high throughput genetic screens with edgeR and Limma's camera function -- great stuff. Now I am wondering whether anybody has already worked through solutions for analyzing time courses. What do you think is the best way for scoring the behavior of multiple gRNAs/s ...
edger high-throughput screening written 11 months ago by knaxerova10
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Answer: A: EdgeR-type analysis for ranked data?
... Thanks so much Aaron. That sounds like a very good approach. I actually already tried to filter out the "bad" reagents to correct the disturbing slope that the data shows in an MA plot, but that also got rid of real signal. Your suggestion is much better. Will try the csaw package asap. ...
written 23 months ago by knaxerova10
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EdgeR-type analysis for ranked data?
... Hi everyone, we normally use EdgeR to analyze sequencing data from genetic screens (i.e. the data is the abundance of a reagent like a barcode or a gRNA under different conditions). This usually works great. However, now I am trying to analyze a challenging data set that has undergone some bottlene ...
edger rank written 23 months ago by knaxerova10

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