User: SplittingInfinity

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Posts by SplittingInfinity

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How to modify eSet classes (specifically for Minfi)
... Dear community, I have identified some missing probes on the EPIC array for my analysis using Minfi. Apparently there is no easy way to update this (no mention about this in tutorial or from google). Naively, I've tried to update the Mset object direct as such: head(featureNames(Mset)) [1] "cg18 ...
minfi eset written 9 days ago by SplittingInfinity0
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Answer: A: conumee error: query intensities not given for all probes.
... I had the same problem as well. In case this may be interesting to others, the temporary measure that I'm doing is finding the overlaps between sample and anno file right after CNV.load: data <- CNV.load(Mset) controls.data <- CNV.load(MsetControls) ### find overlaps ### Mset <- mapToG ...
written 5 months ago by SplittingInfinity0
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Normalising GenomicMethylSet / MethylSet in Minfi
... Hi, I was wondering how should one go about normalising 450K Methylation data from GEO that has unmethylated and methylated signal (the file name state that it is unprocessed). I have tried using readGEORawFile() in minfi and the output object is a GenomicMethylSet, which unfortunately does not mee ...
minfi written 10 months ago by SplittingInfinity0
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Answer: A: Minfi error in reading Basename column
... read.450k() throws the character(0)_Grn.idat error because it couldn't find the file specified in the spreadsheet. One of the most common reason is due to sample sheet format. Look for trailing space or illegal characters in your csv file.   ...
written 15 months ago by SplittingInfinity0

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