User: Davis McCarthy

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Posts by Davis McCarthy

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Answer: A: mRNA-seq cross-species analysis, is it possible?
... Hi Mali It _is_ possible and relatively straight-forward to specify a gene- specific normalization factor with edgeR. The GLM methods in edgeR take an argument called "offset", which can be a matrix (of same size as your matrix of counts) providing the appropriate offset for the negative binomial g ...
written 6.3 years ago by Davis McCarthy260
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Answer: A: edgeR vs DESeq for comparison without replicate
... Dear Sangsoon Analysing count data for significance without replicates is always somewhat problematic. Experience tells us that genomic count data (ChIP-Seq, RNA-Seq, etc.) has substantial variability, more than a Poisson distribution is able to account for. However, if you do not have replicates t ...
written 6.4 years ago by Davis McCarthy260
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Answer: A: How to generate count data with desired overdispersion
... Hi Joao Have you tried the ?rnbinom function? The "size" argument to rbinom() determines the extent of overdispersion. Note that this "size" is the inverse of the dispersion parameter as used in the edgeR package (i.e. size = 1/ dispersion ). So I would consider size=1 to be high overdispersion, si ...
written 6.4 years ago by Davis McCarthy260
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Answer: A: R package for DGE analysis between multiple RNA-Seq samples
... Hi Bruno EdgeR has had GLM methods for many months now. These can be used to perform ANOVA-like analyses (analysis of deviance in GLMs) and can handle any experimental design that can be written as a linear model. The edgeR Users Manual has a worked example of an analysis of a paired design, which ...
written 6.4 years ago by Davis McCarthy260
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edgeR users update to v2.2.5
... Dear edgeR users If you are using the release version of edgeR, please ensure you have updated to the latest release version, edgeR 2.2.5. We caught a bug in exactTest() introduced in v2.2.0 that affects p-values when some rows of the count matrix are all zeros. A recent off-list question prompted ...
edger written 6.5 years ago by Davis McCarthy260
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Comment: C: edgeR - multiple comparisions
... Hi Sridhara I'm glad that is makes sense now. I have made some changes to the documentation in the devel version edgeR to make these points clearer. Hope that will help for the future. Cheers Davis On Jun 1, 2011, at 9:41 AM, Sridhara Gupta Kunjeti wrote: > Hello Davis, > Thank you very m ...
written 6.5 years ago by Davis McCarthy260
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edgeR - multiple comparisions
... Hi Sridhara The function exactTest() has an argument 'pair'. This argument can be used to define the two groups you wish to compare. The order in which you put in the groups in the pair will determine the direction of the log-fold change. For instance if you called > exactTest(d1, common.disp=F ...
epigenetics go edger written 6.5 years ago by Davis McCarthy260 • updated 6.5 years ago by Sridhara Gupta Kunjeti320
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Comment: C: edgeR - multiple comparisions
... Hi Sridhara I'm not sure I completely follow what you're saying about the FDRs being 0.5, 0.6 etc. Can you show us a top table? Output of topTags(). Actually it would be good to see all of your edgeR function calls to get a better idea of how you're carrying out your analysis. In principle I don't ...
written 6.5 years ago by Davis McCarthy260
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Comment: C: edgeR - multiple comparisions
... Hi Sridhara I do not think it is genes with all zero counts for group A and group C are causing the results you see. I just tested this on a dataset with 9 groups, and comparing two groups, A and B, with 285 genes with all zero counts in groups A and B yielded "expected" p-values and FDRs. Therefo ...
written 6.5 years ago by Davis McCarthy260
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Answer: A: EdgeR- equal number of columns per group?
... Hi Lana It certainly should be possible for you to use all of your information. What is the output from dim(D)? Somehow there is a mismatch between the number of columns of your object D and the group labels you are assigning. The group vector you define, c(rep("d45HVC",2),"d45WB"), should indeed ...
written 6.5 years ago by Davis McCarthy260

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