User: davide risso

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davide risso680
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Weill Cornell Medicine
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drisso1893
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Posts by davide risso

<prev • 99 results • page 1 of 10 • next >
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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 11 days ago by davide risso680
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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 15 days ago by davide risso680
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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 15 days ago by davide risso680
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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 17 days ago by davide risso680
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Answer: A: Workflow Perraudeau F1000 - Bioconductor workflow for scRNA-seq
... Hi Viviana, You have changed this line of the workflow: urls = c("https://www.ncbi.nlm.nih.gov/geo/download/?acc=GSE95601&format=file&file= GSE95601%5FoeHBCdiff%5FCufflinks%5FeSet%2ERda%2Egz" "https://raw.githubusercontent.com/rufletch/p63-HBC-diff/master/ref/oeHBCdiff_clusterLabels.txt") W ...
written 8 weeks ago by davide risso680
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Answer: A: Error: In seq_len(ncol(assay)) : first element used of 'length.out' argument
... Hi, if I understand correctly your issue, you need to transform your data.frame into a matrix. sce <- SingleCellExperiment(list(counts=as.matrix(ExprFinal))) should work. If it doesn't, please paste here the results of head(ExprFinal) and we'll try to figure it out. Note that this has nothing t ...
written 3 months ago by davide risso680
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Answer: A: RUVg with differential transcript expression?
... Hi Brian, I have no direct experience with applying RUVSeq factors to a Sleuth analysis, but your code looks reasonable to me. I would examine the distribution of p-values with and without RUV factors in the model to see if it helped (you want to see a uniform distribution plus a spike at 0 corresp ...
written 4 months ago by davide risso680
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Answer: A: Incorporating RUVSeq factors of unwanted variation in DESeq2 time course analysi
... Hi, the example you provided looks good to me. I think that it is sufficient to include W_1 as a main effect in your model. Because you're not testing the effects of W, you have to keep it into the reduced model as well, which is what you did. So everything looks good to me. Note that you are assumi ...
written 5 months ago by davide risso680
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Answer: A: getGeneLengthAndGCContent: "zero or more than one input sequence"
... Hi Mark, I've just tested your code and it works on my machine. Here's what I did: library(EDASeq) tmp <- read.delim("gene_ids.txt", header=FALSE) hsa.len.gc <- getGeneLengthAndGCContent(id=tmp$V1, org="hsa", mode=c("biomart")) and the resulting object > summary(hsa.len.gc) length ...
written 5 months ago by davide risso680
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Comment: C: getGeneLengthAndGCContent: "zero or more than one input sequence"
... It's hard to say what's going on without knowing what are your row names. Can you please provide an example for us to reproduce it and diagnose the problem? For instance, would you be able to share the row names that you're using. How many are they? Is the error still there if you apply the functio ...
written 5 months ago by davide risso680

Latest awards to davide risso

Scholar 11 months ago, created an answer that has been accepted. For A: RUVseq using RUVg most non-differential expressed genes
Scholar 11 months ago, created an answer that has been accepted. For A: effect of polyploidy level on RUVs normalisation
Scholar 11 months ago, created an answer that has been accepted. For A: RUVseq PCA on raw data, whereas DESeq suggests stabilization
Popular Question 11 months ago, created a question with more than 1,000 views. For Workflows in BioC 3.2
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: RUVseq PCA on raw data, whereas DESeq suggests stabilization
Scholar 11 months ago, created an answer that has been accepted. For A: Issue with RUVs
Scholar 15 months ago, created an answer that has been accepted. For A: RUVseq PCA on raw data, whereas DESeq suggests stabilization
Scholar 2.1 years ago, created an answer that has been accepted. For A: RUVseq using RUVg most non-differential expressed genes
Teacher 2.1 years ago, created an answer with at least 3 up-votes. For A: RUVseq PCA on raw data, whereas DESeq suggests stabilization
Scholar 2.1 years ago, created an answer that has been accepted. For A: Normalisation before RUVg and RUV2?
Scholar 2.1 years ago, created an answer that has been accepted. For A: Issue with RUVs
Scholar 2.1 years ago, created an answer that has been accepted. For A: effect of polyploidy level on RUVs normalisation
Scholar 2.1 years ago, created an answer that has been accepted. For A: RUVseq PCA on raw data, whereas DESeq suggests stabilization
Scholar 2.5 years ago, created an answer that has been accepted. For A: Normalisation before RUVg and RUV2?
Teacher 2.5 years ago, created an answer with at least 3 up-votes. For A: RUVseq PCA on raw data, whereas DESeq suggests stabilization
Scholar 2.5 years ago, created an answer that has been accepted. For A: Normalisation before RUVg and RUV2?
Scholar 3.0 years ago, created an answer that has been accepted. For A: Normalisation before RUVg and RUV2?

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