User: davide risso

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davide risso410
Reputation:
410
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Trusted
Location:
Weill Cornell Medicine
Twitter:
drisso1893
Last seen:
1 month, 1 week ago
Joined:
5 years, 8 months ago
Email:
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Posts by davide risso

<prev • 77 results • page 1 of 8 • next >
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Comment: C: Zero inflation in RUV normalization and DE for single cell data
... Well it's not quite like 10 observations since you have data for ~10,000 genes and you can take advantage of the mean-variance relation expected from the negative binomial distribution to look at goodness-of-fit. Anyway, the data are public so you can play around with the data yourself: https://www. ...
written 6 weeks ago by davide risso410
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Comment: C: Zero inflation in RUV normalization and DE for single cell data
... We did a few goodness-of-fit plot and it seemed that the negative binomial model was underestimating the number of zeros. ...
written 6 weeks ago by davide risso410
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Comment: C: Zero inflation in RUV normalization and DE for single cell data
... I'm not sure that sample size has much to do with this. Low amount of RNA and amplification bias seems more relevant. The first scRNA-seq dataset that I worked with had 10 cells and there was no doubt a large amount of zero inflation. Anyway, re: zero-inflation and bulk RNA-seq, this is an interest ...
written 6 weeks ago by davide risso410
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Answer: A: RUVseq: How to implement to more complex time-course model?
... Hi, I'm sorry but from your code is hard to understand what you are trying to do. It seems that there are two different issues: 1. How to choose k. 2. How to compute empirical negative controls. As for 1) we don't have any "magic" formula, the advice is to look at exploratory plots like RLE and ...
written 6 weeks ago by davide risso410
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Answer: A: Zero inflation in RUV normalization and DE for single cell data
... I'll try to answer the first question. I think it is beneficial to consider zero-infated distributions to model single-cell data. In fact, we developed the zinbwave package that implements a zero-inflated negative binomial model. However, we generally use that model for another situation, in which ...
written 6 weeks ago by davide risso410
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Answer: A: Does it make sense to consider RUVr normalization for single cell RNA analysis?
... Hi Nik, I have to admit that I haven't read the Ding et al. paper. I will look at it and come back for a more sensible reply. In the meantime there are a couple of considerations that I think are worth it. RUVr is based on residuals, i.e., it first removes the factor of interest and then look fo ...
written 7 weeks ago by davide risso410
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Comment: C: What to use: PCA or tSNE dimension reduction in DESeq2 analysis?
... Since Mike mentioned the ZINB-WaVE approach, I will add a few more things to my comment on twitter. The advantage of PCA or ZINB-WaVE is that these are factor analysis models, hence there is a clear interpretation of the reduced space in which you do the clustering (in the case of ZINB-Wave, the ma ...
written 12 weeks ago by davide risso410
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Answer: A: RNAseq Analysis using RUVs
... Hi, it is definitely best to combine all the data into one matrix, normalize, and test for differential expression in one go. This will allow you to estimate the variance across all of your samples, which should give you more power. Note that since you are interested in the pairwise differences, y ...
written 12 weeks ago by davide risso410
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Answer: A: Decide normalisation method in RUVseq for RNAseq data
... Hi, which is the "best" normalization is not easy to say, since we don't know the ground truth and in most cases the answer will be dataset dependent. However, there is extensive literature on comparison of normalization approaches, just looking for "RNA-seq normalization" will return many hits in ...
written 3 months ago by davide risso410
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Comment: C: BiocParallel::bplapply() performance with MulticoreParam() is worse than mclappl
... Thanks Martin and Johannes! Both of your suggestions are appreciated! I agree with Martin's point on vectorizing operations, but I came across this behavior and wanted to get your opinion on this. ...
written 3 months ago by davide risso410

Latest awards to davide risso

Scholar 6 months ago, created an answer that has been accepted. For A: RUVseq PCA on raw data, whereas DESeq suggests stabilization
Scholar 17 months ago, created an answer that has been accepted. For A: Normalisation before RUVg and RUV2?
Scholar 17 months ago, created an answer that has been accepted. For A: Issue with RUVs
Scholar 17 months ago, created an answer that has been accepted. For A: effect of polyploidy level on RUVs normalisation
Scholar 17 months ago, created an answer that has been accepted. For A: RUVseq using RUVg most non-differential expressed genes
Scholar 17 months ago, created an answer that has been accepted. For A: RUVseq PCA on raw data, whereas DESeq suggests stabilization
Teacher 17 months ago, created an answer with at least 3 up-votes. For A: RUVseq PCA on raw data, whereas DESeq suggests stabilization
Scholar 22 months ago, created an answer that has been accepted. For A: Normalisation before RUVg and RUV2?
Teacher 22 months ago, created an answer with at least 3 up-votes. For A: RUVseq PCA on raw data, whereas DESeq suggests stabilization
Scholar 22 months ago, created an answer that has been accepted. For A: Normalisation before RUVg and RUV2?
Scholar 2.4 years ago, created an answer that has been accepted. For A: Normalisation before RUVg and RUV2?

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