User: davide risso

gravatar for davide risso
davide risso500
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500
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Weill Cornell Medicine
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drisso1893
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22 hours ago
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5 years, 10 months ago
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r***********@gmail.com

Posts by davide risso

<prev • 86 results • page 1 of 9 • next >
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Answer: A: Error and weird result of TCGAanalyze_Normalization function using the R package
... Hi, I am not familiar with the implementation of TCGAbiolinks and with how they use the functions in the EDASeq package, so I'm not fully able to address your problem. Hopefully, some of the TCGAbiolinks authors / maintainers will chip in. The error seems related to some naming issues. How does your ...
written 22 hours ago by davide risso500
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Answer: A: Outputting batch-effect free normalized counts
... Hi Ilo, From the RUVSeq vignette: The normalized values are stored in the normalizedCounts slot and can be accessed with the normCounts method. The answer to your previous question was also in the vignette. Please, read carefully the RUVSeq vignette before asking questions on the forum. Best, Davi ...
written 13 days ago by davide risso500
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Comment: C: From RleList to RleArray
... Thanks Pete! I knew you could help! I almost just wrote directly to you ;) ...
written 17 days ago by davide risso500
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From RleList to RleArray
... Hi all, is there a way to transform an RleList (or a list of Rle's) into a RleArray / RleMatrix? My use case is that I have a loop / lapply that returns a list of Rle objects that I would like to store as a RleMatrix (each column as an Rle). Minimal example: x <- Rle(10:1, 1:10) rl <- RleList( ...
rle rlelist delayedarray written 17 days ago by davide risso500 • updated 17 days ago by Peter Hickey290
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Answer: A: Differential Expression analysis between distinct scRNA-seq datasets
... I presume that since you are talking about similar numbers of cell types and subpopulations, you have already run some kind of cluster analysis that gave you cluster labels for each of the cells. If that's the case, I would use a differential expression method (for instance MAST) to compare the two ...
written 19 days ago by davide risso500
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Comment: C: Batch effects between controls
... I'm not sure I understand your question. The same way you specify the names of the spike ins, you can specify the names of the endogenous genes that you want to use as negative controls. Section 2.4 of the vignette uses endogenous genes as negative controls. ...
written 20 days ago by davide risso500
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Answer: A: Batch effects between controls
... Hi Ilo, It is expected that upper-quartile normalization will not handle batch effects as it is only a global scaling normalization and is not related to the RUV method. I suggest that you read carefully the RUVSeq vignette if you want to use RUV to try and adjust for batch effects. An alternative ...
written 20 days ago by davide risso500
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Comment: C: RNA Seq analysis vs. Single cell RNA seq analysis
... Another relevant paper: https://www.biorxiv.org/content/early/2017/06/30/157982 ...
written 6 weeks ago by davide risso500
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Answer: A: How to use RUVSeq in clustering problems?
... I'm not sure if this is the only problem, but you should not use RUVs on the rlog transformed values from DESeq2. RUVs assumes that your input matrix contains counts, and rounded transformed data from DESeq2 is not the the expected input for RUVs (which will internally take the log of the counts). ...
written 6 weeks ago by davide risso500
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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 3 months ago by davide risso500

Latest awards to davide risso

Scholar 8 months ago, created an answer that has been accepted. For A: RUVseq PCA on raw data, whereas DESeq suggests stabilization
Scholar 19 months ago, created an answer that has been accepted. For A: Normalisation before RUVg and RUV2?
Scholar 19 months ago, created an answer that has been accepted. For A: Issue with RUVs
Scholar 19 months ago, created an answer that has been accepted. For A: effect of polyploidy level on RUVs normalisation
Scholar 19 months ago, created an answer that has been accepted. For A: RUVseq using RUVg most non-differential expressed genes
Scholar 19 months ago, created an answer that has been accepted. For A: RUVseq PCA on raw data, whereas DESeq suggests stabilization
Teacher 19 months ago, created an answer with at least 3 up-votes. For A: RUVseq PCA on raw data, whereas DESeq suggests stabilization
Scholar 23 months ago, created an answer that has been accepted. For A: Normalisation before RUVg and RUV2?
Teacher 24 months ago, created an answer with at least 3 up-votes. For A: RUVseq PCA on raw data, whereas DESeq suggests stabilization
Scholar 24 months ago, created an answer that has been accepted. For A: Normalisation before RUVg and RUV2?
Scholar 2.5 years ago, created an answer that has been accepted. For A: Normalisation before RUVg and RUV2?

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