User: davide risso

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davide risso830
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University of Padova
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drisso1893
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Posts by davide risso

<prev • 122 results • page 1 of 13 • next >
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Answer: A: Should I use RUVseq on raw counts or on normalized counts coming from EDASeq pac
... Hi, in our experience, it is _usually_ preferable to apply RUV to the normalized counts. However, that means that the assumption of the normalization method hold in your data. In particular, usually normalizations assume that the majority of genes are not DE and/or that there is a roughly equal nu ...
written 3 days ago by davide risso830
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Answer: A: Error: row names supplied are of the wrong length in RUVSeq
... Sorry, I somehow missed this question until now. Are you sure that `filtered` has column names? i.e., what is the result of `colnames(filtered)`? Best, Davide ...
written 4 months ago by davide risso830
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Comment: C: Upper-quartile normalization before RUVg normalization?
... I would perhaps consider filtering out the spike-ins with a lot of zeros and/or choose a different normalization than upper-quartile, more robust to zeros, e.g., TMM or even scran (developed specifically with data with lots of zeros). Alternatively, you can use RUVg without normalizing the data fir ...
written 5 months ago by davide risso830
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Answer: A: Upper-quartile normalization before RUVg normalization?
... Hi Jon, you are right, adjusting for sequencing depth prior to RUV does influence the results. Our recommended workflow is to first run a between-sample normalization (e.g., by using upper-quartile implemented in `betweenLaneNormalization`) to adjust for sequencing depth and then run RUV. This is a ...
written 5 months ago by davide risso830
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Comment: C: Using RUVSeq RUVs() to perform batch correction using technical replicates
... I agree with Gordon, those two groups are indeed worrying, even more so as your technical replicates are all in the top group, so there's no hope that those will help you account for it... As for your original question, increasing k in RUVs() should make the technical replicates closer to each othe ...
written 7 months ago by davide risso830
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Comment: C: normalized counts from RUVg run: is further library size normalization needed?
... Hi Gordon, Sorry, I somehow missed this comment. You are right, the residuals are essentially batch-corrected logCPM values on the log scale. The output from betweenLaneNormalization (EDASeq package) only performs library size normalization (by default with upper-quartile normalization), so they wo ...
written 8 months ago by davide risso830
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Answer: A: How to best represent weights in SummarizedExperiment or SingleCellExperiment?
... Since the weights are a J x N matrix (same dimension of the expression data), the natural thing to do is to create a new assay. This is the approach taken in `DESeq2` and `zinbwave`, which both call this assay simply `weights`. (So to answer your first question `DESeq2` also supports weights, as wel ...
written 8 months ago by davide risso830
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Answer: A: How to remove samples from EDAseq SeqExpressionSeq
... Hi Jon, yes, simply subsetting the `SeqExpressionSet` will subset both expression data and metadata (if by metadata you mean what in ExpressionSet jargon are called phenoData and featureData, i.e., sample and gene metadata). Example: > library(EDASeq) > example("betweenLaneNormaliza ...
written 9 months ago by davide risso830
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Comment: C: normalized counts from RUVg run: is further library size normalization needed?
... Our recommended pipeline is to first account for sequencing depth differences with betweenLaneNormalization() and then run RUV. One can run RUV without library size normalization and hope that one of the factors will account for that. It usually happens, but we find that it's preferable in practice ...
written 11 months ago by davide risso830
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Comment: C: normalized counts from RUVg run: is further library size normalization needed?
... The "normalizedCounts" are simply the residuals of the model, so they are not CPM values, but one can fit the RUV model starting from CPM values. That's our recommended pipeline, except we don't call the result of our betweenLaneNormalization function CPM because we do not scale them to be count per ...
written 11 months ago by davide risso830

Latest awards to davide risso

Scholar 9 months ago, created an answer that has been accepted. For A: RUVseq PCA on raw data, whereas DESeq suggests stabilization
Popular Question 9 months ago, created a question with more than 1,000 views. For BiocParallel::bplapply() performance with MulticoreParam() is worse than mclapply()
Scholar 12 months ago, created an answer that has been accepted. For A: RUVseq PCA on raw data, whereas DESeq suggests stabilization
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: RUVseq PCA on raw data, whereas DESeq suggests stabilization
Scholar 16 months ago, created an answer that has been accepted. For A: RUVseq PCA on raw data, whereas DESeq suggests stabilization
Centurion 16 months ago, created 100 posts.
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 2.3 years ago, created an answer that has been accepted. For A: Issue with RUVs
Teacher 2.3 years ago, created an answer with at least 3 up-votes. For A: RUVseq PCA on raw data, whereas DESeq suggests stabilization
Scholar 2.3 years ago, created an answer that has been accepted. For A: effect of polyploidy level on RUVs normalisation
Scholar 2.3 years ago, created an answer that has been accepted. For A: RUVseq using RUVg most non-differential expressed genes
Scholar 2.3 years ago, created an answer that has been accepted. For A: RUVseq PCA on raw data, whereas DESeq suggests stabilization
Popular Question 2.3 years ago, created a question with more than 1,000 views. For Workflows in BioC 3.2
Scholar 2.6 years ago, created an answer that has been accepted. For A: RUVseq PCA on raw data, whereas DESeq suggests stabilization
Teacher 3.5 years ago, created an answer with at least 3 up-votes. For A: RUVseq PCA on raw data, whereas DESeq suggests stabilization
Scholar 3.5 years ago, created an answer that has been accepted. For A: Issue with RUVs
Scholar 3.5 years ago, created an answer that has been accepted. For A: RUVseq using RUVg most non-differential expressed genes
Scholar 3.5 years ago, created an answer that has been accepted. For A: RUVseq PCA on raw data, whereas DESeq suggests stabilization
Scholar 3.5 years ago, created an answer that has been accepted. For A: Normalisation before RUVg and RUV2?
Scholar 3.5 years ago, created an answer that has been accepted. For A: effect of polyploidy level on RUVs normalisation
Scholar 3.9 years ago, created an answer that has been accepted. For A: Normalisation before RUVg and RUV2?
Teacher 3.9 years ago, created an answer with at least 3 up-votes. For A: RUVseq PCA on raw data, whereas DESeq suggests stabilization
Scholar 3.9 years ago, created an answer that has been accepted. For A: Normalisation before RUVg and RUV2?
Scholar 4.4 years ago, created an answer that has been accepted. For A: Normalisation before RUVg and RUV2?

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