User: davide risso

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davide risso740
Reputation:
740
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Trusted
Location:
Weill Cornell Medicine
Twitter:
drisso1893
Last seen:
2 months, 1 week ago
Joined:
6 years, 8 months ago
Email:
r***********@gmail.com

Posts by davide risso

<prev • 105 results • page 1 of 11 • next >
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Comment: C: Global expression shift using RUVSeq
... That's correct! ...
written 10 weeks ago by davide risso740
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Answer: A: Global expression shift using RUVSeq
... Hi, in the case of a global shift of expression the preliminary scaling step that we show in Section 2.3 should be avoided, as it assumes that the majority of the genes are not DE. In practice, it means to avoid the betweenLaneNormalization and the calcNormFactor steps. You may want to set the all t ...
written 10 weeks ago by davide risso740
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Comment: C: Merging RNAseq Datasets of Different Depths
... Just want to add to Aaron's excellent answer that you may try the scmap Bioconductor package to match your cells to published data. ...
written 3 months ago by davide risso740
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Comment: C: meanVarPlot Ignores Sample Total Count Differences
... I don't think it's reasonable to *require* normalized counts, as one might want to look at the mean variance relation of raw counts. If the object contains normalized counts, `meanVarPlot` will use them. ...
written 3 months ago by davide risso740
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Answer: A: Mean-Variance Plot for Normalised Counts
... This is a bug and should be fixed. I'll take care of this ASAP. normCounts(set) <- measurementsVST should store the normalized counts in the normalizedCounts slot. The meanVarPlot function uses the normalized counts, if available. But of course it looks for it as normalizedCounts not normCounts. ...
written 3 months ago by davide risso740
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Answer: C: Could Not Find Function sizeFactorNames R v3.5
... Hi, I'm not sure why calcAverage does not work for you, as with the current Bioc release versions of the scater and SingleCellExperiment packages it works for me (see below). I would note that you seem to have a mix of release and devel Bioconductor packages: you mention that you are running Biocond ...
written 3 months ago by davide risso740
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Comment: C: use EDAseq normalized data as input of DESeq2
... It looks reasonable, but we haven't tested this approach, so I would carefully look at the results, residuals, etc. to make sure that everything looks reasonable in terms of model fit. It might be good to check with Gordon Smyth or other limma developers. ...
written 4 months ago by davide risso740
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Comment: C: use EDAseq normalized data as input of DESeq2
... Hi Pietro, please use the "comment" function to comment on an answer, and the "answer" function only to add an answer to the original question. I see what you mean now: you are looking for a coercion method to DESeqDataSet similar to the one that we have for CountDataSet. There isn't one because no ...
written 4 months ago by davide risso740
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Answer: A: use EDAseq normalized data as input of DESeq2
... Hi Pietro, first, the DESeq2 vignette can be found at this link. As you will see, Mike did a great job at covering as many use cases as possible and he has a section on how to import gene-specific size factors from EDASeq and similar packages: https://bioconductor.org/packages/release/bioc/vignettes ...
written 4 months ago by davide risso740
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Answer: A: Mean Expression Calculation scRNA-seq (All cells or only Expressed Cells)
... Hi, I'm not too familiar with the monocle differential expression model, but I'll try to answer your question, which seems more general than monocle. There is no consensus yet in the field on the best way to compare the mean expression across conditions. However, there is a very thorough review of ...
written 4 months ago by davide risso740

Latest awards to davide risso

Centurion 3 months ago, created 100 posts.
Scholar 3 months ago, created an answer that has been accepted. For A: RUVseq PCA on raw data, whereas DESeq suggests stabilization
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: RUVseq PCA on raw data, whereas DESeq suggests stabilization
Scholar 15 months ago, created an answer that has been accepted. For A: RUVseq using RUVg most non-differential expressed genes
Scholar 15 months ago, created an answer that has been accepted. For A: effect of polyploidy level on RUVs normalisation
Teacher 15 months ago, created an answer with at least 3 up-votes. For A: RUVseq PCA on raw data, whereas DESeq suggests stabilization
Scholar 15 months ago, created an answer that has been accepted. For A: Issue with RUVs
Popular Question 15 months ago, created a question with more than 1,000 views. For Workflows in BioC 3.2
Scholar 15 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: RUVseq PCA on raw data, whereas DESeq suggests stabilization
Teacher 2.4 years ago, created an answer with at least 3 up-votes. For A: RUVseq PCA on raw data, whereas DESeq suggests stabilization
Scholar 2.4 years ago, created an answer that has been accepted. For A: RUVseq PCA on raw data, whereas DESeq suggests stabilization
Scholar 2.4 years ago, created an answer that has been accepted. For A: RUVseq using RUVg most non-differential expressed genes
Scholar 2.4 years ago, created an answer that has been accepted. For A: effect of polyploidy level on RUVs normalisation
Scholar 2.4 years ago, created an answer that has been accepted. For A: Issue with RUVs
Scholar 2.4 years ago, created an answer that has been accepted. For A: Normalisation before RUVg and RUV2?
Scholar 2.8 years ago, created an answer that has been accepted. For A: Normalisation before RUVg and RUV2?
Teacher 2.8 years ago, created an answer with at least 3 up-votes. For A: RUVseq PCA on raw data, whereas DESeq suggests stabilization
Scholar 2.8 years ago, created an answer that has been accepted. For A: Normalisation before RUVg and RUV2?
Scholar 3.4 years ago, created an answer that has been accepted. For A: Normalisation before RUVg and RUV2?

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