User: Michael Muratet

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Posts by Michael Muratet

<prev • 41 results • page 1 of 5 • next >
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How many biological replicates might suffice with Cox-Reid estimation in DESeq2 (or edgeR)?
... Greetings I am working on analyzing the data from an experiment with multiple technical replicates but no biological replicates. FWIW, it's the same data set I have posted about in recent weeks. I think the experiment would benefit greatly from some biological replicates. The question I have is thi ...
written 6.2 years ago by Michael Muratet420 • updated 6.2 years ago by Michael Love24k
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Analyzing technical replicates with DESeq2
... Hi Simon I've been using DESeq2 to analyze RNA-seq data I was given for a multi-factor experiment, three factors with two, three and three levels each with three 'replicates' in each cell. I recently learned that the replicates are actually technical, not biological, and I'm looking for the best wa ...
normalization deseq2 written 6.3 years ago by Michael Muratet420 • updated 6.3 years ago by Ryan C. Thompson7.3k
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Comment: C: Interpreting DESeq2 results
... On Apr 10, 2013, at 2:49 PM, Michael Love wrote: > Hi Michael, > > Yes, log2FoldChange is the value of the coefficient/beta. The model and coefficients are described in Section B in the vignette. > > log2(mu) = beta_intercept + beta_day14 * x_day14 + ... > log2(mu) = 12.11 - 0.06 ...
written 6.4 years ago by Michael Muratet420
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Interpreting DESeq2 results
... On Mar 28, 2013, at 4:19 PM, Michael Love wrote: > Hi Michael, > > The baseMean column is not on the log scale; it is the mean of normalized counts for a gene. The intercept from the GLM is labelled intercept in mcols(dse). > > Mike > Hello again Here's a snippet of output for t ...
written 6.4 years ago by Michael Muratet420 • updated 6.4 years ago by Michael Love24k
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Interpreting DESeq2 results
... Greetings I have an experiment: > design(dse) ~ factor1 + factor2 + factor3 where factor1 has two levels, factor2 has three levels and factor3 has three levels. I extract a gene of interest from the results for each term (I've changed the indices to reflect the condition): > lapply(results ...
written 6.4 years ago by Michael Muratet420 • updated 6.4 years ago by Michael Love24k
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Comment: C: Multifactor analysis with deseq
... Howdy I just ran DESeq(des) for the first time and got thousands of lines of output, which explains the length of the vignette. Looking for the parameter to turn it off.... ;-) Cheers Mike Michael Muratet, Ph.D. Senior Scientist HudsonAlpha Institute for Biotechnology mmuratet at hudsonalpha.org ...
written 6.4 years ago by Michael Muratet420
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Comment: C: Multifactor analysis with deseq
... On Mar 25, 2013, at 1:36 PM, Simon Anders wrote: > Hi > > [Please keep conversations on the list.] Sorry, upgraded my OS X and didn't realize there is now a separate button for 'reply all'. Progress. > >> I tried to install deseq2 and discovered I need R 2.16. CRAN only >> ...
written 6.4 years ago by Michael Muratet420
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Multifactor analysis with deseq
... Dear Dr Anders I have a few questions about applying deseq to a multifactor analysis that I am doing. I have three factors: three levels of genotype, three levels of "cell culture" and two time points. I have three replicates in each cell. The comparison(s) of most interest are changes in expressio ...
normalization deseq deseq2 written 6.4 years ago by Michael Muratet420 • updated 6.4 years ago by Simon Anders3.6k
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Comment: C: Selecting elements in GRanges object by element metadata
... On Jul 11, 2012, at 10:21 AM, Kasper Daniel Hansen wrote: > What you are reporting is true for any (well, there may be exceptions > I guess) subsetting. Try for example with a standard matrix. The > solution is to add which(). Contrast > >> x = c(1,2,NA) >> x == 2 > [ ...
written 7.1 years ago by Michael Muratet420
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Selecting elements in GRanges object by element metadata
... Greetings I would like to select elements from a GRanges object by testing values in the metadata columns. This seems to work OK: x.gr[which(elementMetadata(x.gr)$fdr<0.05)] So does this, although there's nothing in the documentation about the [] operator accepting logical values: fosl2.th17. ...
written 7.1 years ago by Michael Muratet420 • updated 7.1 years ago by Michael Lawrence11k

Latest awards to Michael Muratet

Popular Question 6.2 years ago, created a question with more than 1,000 views. For Interpreting DESeq2 results
Popular Question 6.2 years ago, created a question with more than 1,000 views. For RNAseq expression analysis using DESeq: technical replicates, paired samples
Popular Question 6.2 years ago, created a question with more than 1,000 views. For Interpreting DESeq2 results
Popular Question 6.2 years ago, created a question with more than 1,000 views. For Selecting elements in GRanges object by element metadata
Popular Question 6.2 years ago, created a question with more than 1,000 views. For Multifactor analysis with deseq
Popular Question 6.2 years ago, created a question with more than 1,000 views. For Selecting elements in GRanges object by element metadata

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