User: DonnyB

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DonnyB0
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Posts by DonnyB

<prev • 11 results • page 1 of 2 • next >
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Comment: C: ELMER::createMAE() Error: $ operator is invalid for atomic vectors
... That seems to have sorted it, thanks! ...
written 4 weeks ago by DonnyB0
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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 4 weeks ago by DonnyB0
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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 4 weeks ago by DonnyB0
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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 4 weeks ago by DonnyB0
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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 4 weeks ago by DonnyB0
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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 5 weeks ago by DonnyB0
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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 5 weeks ago by DonnyB0 • updated 5 weeks ago by James W. MacDonald50k
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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 8 months ago by DonnyB0 • updated 8 months ago by Yuan Tian110
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Comment: C: EdgeR - blocking for multiple factors at once - Errors
... Thanks! Much appreciated. Dean ...
written 9 months ago by DonnyB0
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EdgeR - blocking for multiple factors at once - Errors
... Hi all, I'm performing a DE analysis on RNAseq data using EdgeR. I have a number of samples each with: untreated, treatmentA, treatmentB My samples are split across two batches. My metadata therefore looks something like this : Treatment Patient Batch UT 1 1 ...
edger multiple factor design blocked design written 9 months ago by DonnyB0 • updated 9 months ago by Aaron Lun24k

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