User: Mark Robinson

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Mark Robinson870
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Posts by Mark Robinson

<prev • 85 results • page 2 of 9 • next >
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Answer: A: edgeR glmFit
... Hi Jahn, I've cc'd the BioC mailing list; it's best to keep a public record of these exchanges, so others can benefit. So, I believe your problem is a matter of the class of the object that you are sending to estimateGLMCommonDisp(), etc.. Here is an example: > y <- matrix(rnbinom(1000,mu= ...
written 5.7 years ago by Mark Robinson870
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Answer: A: calcNormFactors gives NaN normalization values- Please Help!
... Hi Audra, Your dataset looks pretty sparse (a lot of 0s), which is ok but it could be due to this: ---- ?calcNormFactors If ?refColumn? is unspecified, the library whose upper quartile is closest to the mean upper quartile is used. ---- As you can see, many of your upper quartiles are 0 or 1 and ...
written 5.7 years ago by Mark Robinson870
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Answer: A: edgeR glmFit
... Hi Jahn, Chapter 3 demonstrates the setup of design matrices; 3.1 says "In this chapter, we outline the principles for setting up the design matrix and forming contrasts for some typical experimental designs". You would then combine that with what is shown in "1.4 Quick start" to do all the steps, ...
written 5.7 years ago by Mark Robinson870
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Answer: A: edgeR DGEList
... Hi Jahn, I've cc'd the list. Look, a lot of people say that you must must must have raw counts for this and strictly, this is true. My view is that as long as there are not too too many ambiguous reads, then this portioning off of reads in a non-integer fashion to features will not create such a ...
written 5.7 years ago by Mark Robinson870
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Answer: A: edgeR DGEList
... Jahn: Load the package first ? library("edgeR") dge <- DGEList(counts=cots) ? Best, Mark On 12.12.2013, at 09:35, Jahn Davik [guest] wrote: > > Hi there, > I am trying to import the counts data (='cots', count data set generated in Trinity) into R. When I run > $ dge<-DGELis ...
written 5.7 years ago by Mark Robinson870
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Answer: A: edgeR - 3-dimensional Multidimensional scaling
... Dear Paraskevas, Maybe all you need is to set 'ndim=3' in your call to plotMDS() ? > However, the 2D plot obtained with cmdscale using the counts per million ( cpm ) is much different compared to that obtained with plotMDS . Have a careful read of: ?plotMDS.DGEList ?plotMDS In short, plotMDS ...
written 5.7 years ago by Mark Robinson870
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Answer: A: confused with edgeR: multiple groups vs one control
... Dear Joel, > For what I know, mutations in genA and genB produce similar phenotypes and some Northern blots confirm that miR156 is upregulated in those mutations compared to WT, while miR172 is downregulated compared to WT, yet in my results the logFC of miR156 is close to 0.5 for genA and -0.1 ...
written 5.7 years ago by Mark Robinson870
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Answer: A: Too many DEG with edgeR output?
... Hi Bernardo, A couple quick notes. 1. Filtering > keep <- rowSums(cpm(RG)>1) >= 2 #we keep genes that achieve at least one > count per million (cpm) in at least three samples Despite what the comment says, this keeps only features where CPM=1 or higher in BOTH of your samples. Bu ...
written 5.8 years ago by Mark Robinson870
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Answer: A: Bioconductor: CPM and log(CPM) values in EdgeR does not match
... Dear Christian, I think you want base 2: > 2^1.80454 [1] 3.493178 > 2^(12.11638) [1] 4440.111 Best, Mark ---------- Prof. Dr. Mark Robinson Bioinformatics, Institute of Molecular Life Sciences University of Zurich http://tiny.cc/mrobin On 01.08.2013, at 09:08, CSRK (Christian Schr?der ...
written 6.1 years ago by Mark Robinson870
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Answer: A: edgeR dispersion value
... Hi Tiago, Just a quick comment ? when the manual is talking about "Typical values for the common BCV ?", that is in the context of analyses with no replicates. You do not mention whether you have replicates, but if you do, then it is generally better to use them to estimate the dispersion. If you ...
written 6.1 years ago by Mark Robinson870

Latest awards to Mark Robinson

Popular Question 5.0 years ago, created a question with more than 1,000 views. For counting RNA-seq reads in R/BioC
Popular Question 5.0 years ago, created a question with more than 1,000 views. For Postdoc in Statistical Bioinformatics, Zurich, Switzerland

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