User: davide risso

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davide risso350
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350
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University of California, Berkeley, USA
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drisso1893
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6 days ago
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Posts by davide risso

<prev • 65 results • page 1 of 7 • next >
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Answer: A: How to determine a set of empirical control 'genes' using RUVSeq
... Of course 5000 should not be considered as a one-fits-all number. We just empirically found that that number of genes was OK in that dataset. The first question is whether there are stable repeats to start with. Could it be that all the repeats are influenced by the KO? Assuming the answer is no, ...
written 7 weeks ago by davide risso350
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Answer: A: Can FPKM or TPM values be used as RUVs input ?
... Hi Wei, RUVSeq is designed to work with gene-level counts. If you are working with TPM or FPKM quantities, you may want to use the ruv package on CRAN or the RUVnormalize package in Bioconductor, depending if you have a supervised or unsupervised problem. Although these packages were designed for ...
written 11 weeks ago by davide risso350
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Answer: A: Appropriate to apply RUVSeq to exon bin counts for DEXSeq?
... Hi Adam, sorry for the late response. Provided that you can identify negative control exons, I don't see any problem with applying RUVSeq to exon data. You should be able to pass the factors of unwanted variation to DEXSeq in the design matrix, in a similar way as you would do with DESeq. We had s ...
written 11 weeks ago by davide risso350
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Answer: A: Raw read count Vs EdgeR normzlized read count for RUVg normalization
... Dear Venu, please note that in our paper (and experience) we see that often normalizing the data using the ERCC spike ins as negative controls does not work as well as using endogenous genes, so it's not surprising that your RLE plots don't look great after RUVg with ERCC as negative controls. Do ...
written 5 months ago by davide risso350
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Answer: A: Fisher exact test
... The way you populate the 2x2 table is, for some definition of differential expression (DE): DE genes in set | non DE genes in set ----------------------- | ---------------------- DE genes not in set | non DE genes not in set You can then use the `fisher.test` function to obtain the ...
written 6 months ago by davide risso350
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Comment: C: Can Normalized cpm values be used as RUVs input
... Let me rephrase that: the value in W are actually informative, but not in an absolute scale, i.e., they're only informative in relation to one another and not for their actual value. ...
written 7 months ago by davide risso350
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Comment: C: Can Normalized cpm values be used as RUVs input
... The values in W are not very informative: Since we need to estimate both W and alpha, these are unidentifiable (e.g., swapping signs between alpha and W will give you the same solution). Increasing k too much may be a problem, especially if the negative control genes are not a perfect set (we genera ...
written 7 months ago by davide risso350
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Answer: A: Can Normalized cpm values be used as RUVs input
... I believe that your approach is reasonable for exploratory data analysis. As you point out, we recommend a different approach for differential expression, but your proposed solution will work if the objective is data exploration.   ...
written 7 months ago by davide risso350
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Answer: A: How to use RUVseq with voom-limma for differential expression analysis?
... Just to integrate Aaron's answer, note that RUVSeq was designed specifically with a negative binomial model in mind. Hence, it is appropriate to use with edgeR and DESeq / DESeq2, but its behavior with limma/voom was never tested. However, the RUV methodology was first developed in a linear model s ...
written 7 months ago by davide risso350
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Comment: C: How to use RUVseq with voom-limma for differential expression analysis?
... I agree with Aaron, normalization and the base of the log function will not affect too much your results and that the choice of the coefficient in topTable is the real issue here. You're effectively testing for genes that are associated with either the factor of interest or the factors of unwanted v ...
written 7 months ago by davide risso350

Latest awards to davide risso

Scholar 7 weeks ago, created an answer that has been accepted. For A: RUVseq PCA on raw data, whereas DESeq suggests stabilization
Scholar 12 months ago, created an answer that has been accepted. For A: Normalisation before RUVg and RUV2?
Scholar 12 months ago, created an answer that has been accepted. For A: Issue with RUVs
Scholar 12 months ago, created an answer that has been accepted. For A: effect of polyploidy level on RUVs normalisation
Scholar 12 months ago, created an answer that has been accepted. For A: RUVseq using RUVg most non-differential expressed genes
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: Normalisation before RUVg and RUV2?
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 17 months ago, created an answer that has been accepted. For A: Normalisation before RUVg and RUV2?
Scholar 23 months ago, created an answer that has been accepted. For A: Normalisation before RUVg and RUV2?

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