User: davide risso

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davide risso810
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Weill Cornell Medicine
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drisso1893
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1 day, 9 hours ago
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Posts by davide risso

<prev • 117 results • page 1 of 12 • next >
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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 1 day ago by davide risso810
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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 5 days ago by davide risso810
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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 7 days ago by davide risso810
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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 10 weeks ago by davide risso810
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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 10 weeks ago by davide risso810
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Comment: C: EDASeq, RUVSeq and edgeR together
... Sorry, I was assuming that you were familiar with the notation we use in RUV, where $W$ is the matrix with the unwanted variation factors and $\alpha$ its associated parameter vector. $Y - W \alpha$ essentially means to look at the coefficient estimates related to the unwanted variation factors in ...
written 11 weeks ago by davide risso810
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Answer: A: normalized counts from RUVg run: is further library size normalization needed?
... Hi, if you follow the workflow described in the RUVSeq vignette, you will perform library size normalization as a first step and RUVg as a second step to normalize the data. If that's the case, then the normalized counts from RUVg are indeed normalized for library size and no further normalization i ...
written 11 weeks ago by davide risso810
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Answer: A: determine k during RUVSeq
... Hi, we haven't found a good way to estimate K in RUV, but exploratory data analysis can be helpful to choose a reasonable value for K. My answer to this thread may be relevant (minus the time course aspect): https://support.bioconductor.org/p/99054/#99077 ...
written 11 weeks ago by davide risso810
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Comment: C: EDASeq, RUVSeq and edgeR together
... You can of course look at the "corrected" values once you fit the model, by looking at $Y - W alpha$, or you could plot the fitted values for the model instead of the observed data. Note that neither RUV nor any other statistical method will tell you if the difference is biological or technical if ...
written 12 weeks ago by davide risso810
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Comment: C: EDASeq, RUVSeq and edgeR together
... Hi Pietro, the issue here is in the terminology. What edgeR calls "logFC" is not a log-fold-change per se but the estimated value of the particular contrast based on the estimates of the coefficient of the regression model. When you use the additional covariates from RUV, you are changing the valu ...
written 12 weeks ago by davide risso810

Latest awards to davide risso

Scholar 3 months ago, created an answer that has been accepted. For A: RUVseq PCA on raw data, whereas DESeq suggests stabilization
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: RUVseq PCA on raw data, whereas DESeq suggests stabilization
Centurion 7 months ago, created 100 posts.
Scholar 7 months ago, created an answer that has been accepted. For A: RUVseq PCA on raw data, whereas DESeq suggests stabilization
Teacher 8 months ago, created an answer with at least 3 up-votes. 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 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
Popular Question 19 months ago, created a question with more than 1,000 views. For Workflows in BioC 3.2
Scholar 23 months ago, created an answer that has been accepted. For A: RUVseq PCA on raw data, whereas DESeq suggests stabilization
Scholar 2.7 years ago, created an answer that has been accepted. For A: Normalisation before RUVg and RUV2?
Teacher 2.7 years ago, created an answer with at least 3 up-votes. For A: RUVseq PCA on raw data, whereas DESeq suggests stabilization
Scholar 2.7 years ago, created an answer that has been accepted. For A: RUVseq PCA on raw data, whereas DESeq suggests stabilization
Scholar 2.7 years ago, created an answer that has been accepted. For A: effect of polyploidy level on RUVs normalisation
Scholar 2.7 years ago, created an answer that has been accepted. For A: RUVseq using RUVg most non-differential expressed genes
Scholar 2.7 years ago, created an answer that has been accepted. For A: Issue with RUVs
Scholar 3.1 years ago, created an answer that has been accepted. For A: Normalisation before RUVg and RUV2?
Teacher 3.2 years ago, created an answer with at least 3 up-votes. For A: RUVseq PCA on raw data, whereas DESeq suggests stabilization
Scholar 3.2 years ago, created an answer that has been accepted. For A: Normalisation before RUVg and RUV2?
Scholar 3.7 years ago, created an answer that has been accepted. For A: Normalisation before RUVg and RUV2?

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