User: D

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D0
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Posts by D

<prev • 13 results • page 1 of 2 • next >
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Comment: C: EdgeR - Complex design - contrasts/coefficients
... Thanks for your very informative answer! For future reference, do you know of a resource which further explores how to deduce the meanings of the coefficients, such that when planning future experiments I do not need to ask for further clarification? Kind regards and many thanks, Dean ...
written 4 weeks ago by D0
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EdgeR - Complex design - contrasts/coefficients
... Hi, I have a question about contrasts for more complex GLM models in edgeR. Taking the section 3.5 example as a starting point ``` > targets <- data.frame(Disease = factor(rep(c("Healthy","Disease1","Disease2"), each = 6)), + Patient = factor(rep(c(1:9), each=2)), + ...
edger glm written 4 weeks ago by D0 • updated 4 weeks ago by Yunshun Chen490
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Comment: C: ELMER::createMAE() Error: $ operator is invalid for atomic vectors
... That seems to have sorted it, thanks! ...
written 3 months ago by D0
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Comment: C: ELMER::createMAE() Error: $ operator is invalid for atomic vectors
... Hi Tiago, Thanks for your reply, unfortunately it appears to be the same (versions are now ELMER_2.9.2, ELMER.data_2.9.3 ) > library(ELMER) > # example input > met <- matrix(rep(0,15),ncol = 5) > colnames(met) <- c("Sample1", + "Sample2", ...
written 3 months ago by D0
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Comment: C: File type for DEseq using ATACseq data
... We use a counts matrix by peak number. Do you only have 1 sample in each group? ...
written 3 months ago by D0
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ELMER::createMAE() Error: $ operator is invalid for atomic vectors
... Hi all, I'm trying to get ELMER running on some of my own EPIC/RNAseq data but first I need to get the example working. I'm encountering an error simply following the example, am I missing packages? (sessioninfo below): > library(ELMER) > # example input > met <- matrix(r ...
elmer written 3 months ago by D0
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Comment: C: EdgeR - Model matrix for complex model similar to user guide 3.5 example - but m
... Thanks both, very helpful! Kind regards, Dean ...
written 3 months ago by D0
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Comment: C: EdgeR - Model matrix for complex model similar to user guide 3.5 example - but m
... Hi, I figured fitting appropriate multifactor GLM was common to all packages, rather than specific to edgeR. Apologies nonetheless. ...
written 3 months ago by D0
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EdgeR - Model matrix for complex model similar to user guide 3.5 example - but more complex
... Hi all, I'm trying to analyse some RNAseq data which has been generated using an experimental design not dissimilar to the example in the user guide (section 3.5, p41), but with some differences that are making applying that model difficult. My study design: > Pheno_mat disease Pati ...
limma edger written 3 months ago by D0 • updated 3 months ago by James W. MacDonald51k
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EPIC methylation array - analysis with ChAMP - how to export bed/wig file to view in UCSC/IGV?
... Hi, I have analysed some Infinium EPIC array, methylation data using ChAMP. I'd like to export the beta values as bed/wig/whatever to view in UCSC/IGV along side some RNAseq data. Is there an off the shelf function to do this (because I can't find one) or am I stuck with writing my own? Cheers,   ...
champ methylation epic written 11 months ago by D0 • updated 11 months ago by Yuan Tian120

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