User: Cittaro Davide

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Posts by Cittaro Davide

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Comment: C: tagwise parameters for negative binomial distribution in edgeR
... On 21/mar/2014, at 01:47, Gordon K Smyth wrote: >> >> Mmm, actually I would like to identify the sample that is an outlier for >> a specific gene, that's why I thought I could focus on tagwise >> distribution. > > See Mark Robinson's post. > > It depends on your ...
written 5.4 years ago by Cittaro Davide240
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Comment: C: tagwise parameters for negative binomial distribution in edgeR
... Hi Mark, Thanks for the comment. On 20/mar/2014, at 14:58, Mark Robinson wrote: > You'd want >= 3 replicates per condition for this one though. > Unfortunately my dataset is made of >200 unique samples :-( What should I expect (except for a ton of warnings...)? I'm going to read ever ...
written 5.4 years ago by Cittaro Davide240
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Comment: C: tagwise parameters for negative binomial distribution in edgeR
... Dear Gordon, thanks for the answer. On 20/mar/2014, at 01:04, Gordon K Smyth wrote: > Dear Davide, > > Do you want to identify tags (genes) with dispersion values that are so > high (relative to other genes with similar count sizes) that they should > be considered outliers? Mmm, ...
written 5.4 years ago by Cittaro Davide240
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tagwise parameters for negative binomial distribution in edgeR
... Dear list, I have a DGElist object in edgeR, already processed with calcNormFactors, estimateCommonDispersion and estimateTagWiseDispersion. Now, I would like to identify tagwise outliers in my data, I thought I could estimate NB distribution for each tag. Given that a NB is defined by two parameter ...
edger written 5.4 years ago by Cittaro Davide240 • updated 5.4 years ago by Gordon Smyth38k
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Comment: C: DEseq for chip-seq data normalisation
... Dear Lucia, On 05/nov/2013, at 13:57, Giuseppe Gallone wrote: >> I do not recommend doing the peak calling with the pooled data.After >> doing several ChIP-seq experiments with replicates I have observed that >> a lot of peaks, even ones with high z-scores/low p-values, do not s ...
written 5.8 years ago by Cittaro Davide240
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Comment: C: [DESeq] p-value vs adjusted p-value
... On Jun 5, 2013, at 8:56 PM, Simon Anders wrote: > On 05/06/13 17:06, lucia kwak wrote: >> Hi all, >> >> Thank you for your answer. I've used method=blind to estimate the >> dispersions in DESeq. For the comparison of tools, I am using different >> p-value cutoff f ...
written 6.2 years ago by Cittaro Davide240
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Comment: C: [DESeq] p-value vs adjusted p-value
... On Jun 5, 2013, at 4:25 PM, Steve Lianoglou wrote: > > > It's not clear to me what you are saying. Are you suggesting that edgeR is > returning a large number of significant genes at a low FDR, or are the > number of significant genes roughly the same at the same FDR's between the & ...
written 6.2 years ago by Cittaro Davide240
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cpm on normalised counts (was "DESeq normalisation strategy")
... Hi Simon, On May 29, 2013, at 11:46 AM, Simon Anders wrote: > The notion of "calculating cpm on normalized counts" is hence a > contradiction in terms. Would you like to expand this sentence? I see it is not uncommon to evaluate counts in cpm after normalization. I'm thinking at edgeR and ...
normalization edger deseq written 6.2 years ago by Cittaro Davide240
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Comment: C: DESeq normalisation strategy
... Hi Simon, On May 29, 2013, at 11:46 AM, Simon Anders wrote: > Hi Davide > > On 29/05/13 10:58, Davide Cittaro wrote: >> I've been reading about DESeq normalization strategy and, as far as I understand, it works on a sample basis: counts for each samples are normalized according to ...
written 6.2 years ago by Cittaro Davide240
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DESeq normalisation strategy
... Dear list, I've been reading about DESeq normalization strategy and, as far as I understand, it works on a sample basis: counts for each samples are normalized according to a factor calculated using the geometric mean of the counts. Three questions: - is this strategy robust when comparing samples w ...
normalization deseq written 6.2 years ago by Cittaro Davide240 • updated 6.2 years ago by Simon Anders3.6k

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Popular Question 5.4 years ago, created a question with more than 1,000 views. For edgeR: counts or pseudo.counts?

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