User: davide risso

gravatar for davide risso
davide risso780
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780
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Weill Cornell Medicine
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drisso1893
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6 days, 18 hours ago
Joined:
6 years, 9 months ago
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Posts by davide risso

<prev • 114 results • page 1 of 12 • next >
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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 6 days ago by davide risso780
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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 6 days ago by davide risso780
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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 7 days ago by davide risso780
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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 7 days ago by davide risso780
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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 9 days ago by davide risso780
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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 19 days ago by davide risso780
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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 19 days ago by davide risso780
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Answer: A: nbinomLRT function all cores usage
... Ciao Matteo, as you can see from your sessionInfo(), you are using a non-default implementation of the BLAS algebra library (specifically the Microsoft/Revolution implementation). This implementation uses parallel computation and, by default, uses all available cores. Obviously, DESeq2 is doing some ...
written 19 days ago by davide risso780
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Answer: A: EDASeq, RUVSeq and edgeR together
... Hi Pietro, I think that your code is fine. And yes, it's likely better to have a tagwise and possibly trended dispersion and not a global dispersion parameter. I believe that edgeR now offers a simpler wrapper function to carry out the three steps that you describe. Have a look at ?edgeR::estimateDi ...
written 6 weeks ago by davide risso780
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Comment: C: Global expression shift using RUVSeq
... That's correct! ...
written 4 months ago by davide risso780

Latest awards to davide risso

Scholar 6 weeks ago, created an answer that has been accepted. For A: RUVseq PCA on raw data, whereas DESeq suggests stabilization
Teacher 6 weeks ago, created an answer with at least 3 up-votes. For A: RUVseq PCA on raw data, whereas DESeq suggests stabilization
Centurion 5 months ago, created 100 posts.
Scholar 5 months ago, created an answer that has been accepted. For A: RUVseq PCA on raw data, whereas DESeq suggests stabilization
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: RUVseq PCA on raw data, whereas DESeq suggests stabilization
Teacher 16 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: Issue with RUVs
Scholar 16 months ago, created an answer that has been accepted. For A: effect of polyploidy level on RUVs normalisation
Scholar 16 months ago, created an answer that has been accepted. For A: RUVseq using RUVg most non-differential expressed genes
Scholar 16 months ago, created an answer that has been accepted. For A: RUVseq PCA on raw data, whereas DESeq suggests stabilization
Popular Question 16 months ago, created a question with more than 1,000 views. For Workflows in BioC 3.2
Scholar 20 months ago, created an answer that has been accepted. For A: RUVseq PCA on raw data, whereas DESeq suggests stabilization
Scholar 2.6 years ago, created an answer that has been accepted. For A: Normalisation before RUVg and RUV2?
Teacher 2.6 years ago, created an answer with at least 3 up-votes. For A: RUVseq PCA on raw data, whereas DESeq suggests stabilization
Scholar 2.6 years ago, created an answer that has been accepted. For A: RUVseq PCA on raw data, whereas DESeq suggests stabilization
Scholar 2.6 years ago, created an answer that has been accepted. For A: effect of polyploidy level on RUVs normalisation
Scholar 2.6 years ago, created an answer that has been accepted. For A: RUVseq using RUVg most non-differential expressed genes
Scholar 2.6 years ago, created an answer that has been accepted. For A: Issue with RUVs
Scholar 3.0 years ago, created an answer that has been accepted. For A: Normalisation before RUVg and RUV2?
Teacher 3.0 years ago, created an answer with at least 3 up-votes. For A: RUVseq PCA on raw data, whereas DESeq suggests stabilization
Scholar 3.0 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: Normalisation before RUVg and RUV2?

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