User: Mark Robinson

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Mark Robinson1.1k
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Posts by Mark Robinson

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Comment: C: edgeR - multiple comparisions
... Hi Sridhara, The problem here is that the output of topTags() (your 'fdr06') is not a data.frame or matrix, which is what write.table() works best on. Instead, try: fdr06 <- topTags(de06.tgw, n = nrow(de06.tgw), adjust.method = "BH", sort.by="p.value") write.table(fdr06$table, file = "FDR06.csv ...
written 6.5 years ago by Mark Robinson1.1k
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Answer: A: edgeR - multiple comparisions
... Hi Sridhara, If you haven't already, you might have a solid read of the edgeR user's guide, it has answers to some of your questions. On May 21, 2011, at 11:20 PM, Sridhara Gupta Kunjeti wrote: > Hello, > I have used edgeR for DGE analysis and I have few questions regarding the > model ...
written 6.5 years ago by Mark Robinson1.1k
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Answer: A: RNA-Seq/edgeR reproducability between lanes
... Hi Lana, On May 12, 2011, at 2:38 AM, Lana Schaffer wrote: > Hi, > I need to state the reproducibility between sequence lanes for RNA- Seq. > I don't think that I can print out a normalized set of count data using TMM but > Just the normalization scale factors? Well, you can do it ma ...
written 6.5 years ago by Mark Robinson1.1k
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Comment: C: calcNormFactors - normalization
... On 2011-05-07, at 9:57 AM, Lana Schaffer wrote: > Mark, > My gene library contains only 141 genes. Is this low number > Alright in this model? Yes, this is alright. For one thing, you pay a much smaller multiple testing penalty. > The length on the genes are not accounted for in th ...
written 6.6 years ago by Mark Robinson1.1k
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Answer: A: calcNormFactors - normalization
... Hi Lana, The factor (offset) that gets used in the statistical model is actually the *product* of lib.size and norm.factors, so the lower depth of library HCV_100d_2 is taken into account. Mark On 2011-05-07, at 9:49 AM, Lana Schaffer wrote: > Greetings, > Using d <- calcNormFactors(d) ...
written 6.6 years ago by Mark Robinson1.1k
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Answer: A: EdgeR GLM gene expression analysis of 3 groups
... Hi Shona. 1. Your counts aren't integers. edgeR expects raw counts. 2. My guess is you don't really need a sample-specific effect. Try: design <- model.matrix(~ age, data = targets) Cheers, Mark On 2011-03-24, at 10:35 PM, Shona Wood wrote: > Hi, > > I have been trying to compa ...
written 6.7 years ago by Mark Robinson1.1k
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Comment: C: edgeR
... Try using one 'DGEList' with all your data, (all the usual steps,) then choose what pair you want to test with: de.3 <- exactTest(d, pair=c("F0","F3")) de.6 <- exactTest(d, pair=c("F0","F6")) Also see ?exactTest and the user's guide. Cheers, Mark > In continuation with my previous emai ...
written 6.7 years ago by Mark Robinson1.1k
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Comment: C: edgeR - tagwise dispersion
... Maybe you've made a typo? How about trying: de.tagwise06 <- exactTest(dt06, common.disp = FALSE) ... since the 'd06' object doesn't have the tagwise dispersions. Also, when you report errors, it's handy to also give the output of traceback() and sessionInfo(). No need in this case, of cours ...
written 6.7 years ago by Mark Robinson1.1k
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Answer: A: edgeR - tagwise dispersion
... Hi Sridhara. You do need to run estimateCommonDisp() before estimateTagwiseDisp(). We've modified the code now to detect whether it has been run and if not, invisibly call it. Mark On 2011-03-04, at 1:03 PM, Sridhara Gupta Kunjeti wrote: > Hi, > I am using edgeR for DGE analysis and I have ...
written 6.7 years ago by Mark Robinson1.1k
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Answer: A: edgeR: calcNormFactors
... Hi Guoli. Use R 2.11.x or greater (2.12.x preferred), install edgeR through biocLite() [http://bioconductor.org/install/] and you will have access to calcNormFactors(). Hope that helps. Mark On 2011-02-24, at 9:00 AM, Wang, Guoli (NIH/CIT) [C] wrote: > I could not run calcNormFactors in edgeR ...
written 6.7 years ago by Mark Robinson1.1k

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