User: annabelle.congras

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Posts by annabelle.congras

<prev • 5 results • page 1 of 1 • next >
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Answer: A: multiple comparison using limma
... Hi,  Thanks for your answers! You were right Aaron I might have done something wrong cause it's working fine now after removing all data and re-running my script line by line.. thanks anyway  James,I actually used minfi for the normalisation/filtering steps, limma for DMP analysis, and I'm now mo ...
written 2.2 years ago by annabelle.congras10
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multiple comparison using limma
... Hi,  I am using limma to get differentially methylated probes from MethylEPIC data, using M values. I have 9 groups of samples (from groupA to group I) within 3 arrays, containing 2 to 5 samples each.  I get very different results depending on the number of comparison I perform ie the number of co ...
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Answer: A: MINFI missing samples in qcreports and densityplots
... Hi again,  Actually if I don't provide any of the sampName and sampGroup options, the densityplots and densitybeanplots in my qcreport are all empty.. does it help understanding the problem? ...
written 2.3 years ago by annabelle.congras10
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Answer: A: MINFI missing samples in qcreports and densityplots
... Hi Kasper, thanks for your answer. The pheno object is complete. Moreover I have the same issue when I use targets$SampleName instead  pheno$SampleName in qcReport or densityPlots.  About that object, is this normal that I obtain 2 different output when using pData (data.frame) or phenoData (Forma ...
written 2.3 years ago by annabelle.congras10
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MINFI missing samples in qcreports and densityplots
... Hello everybody,  I am using Minfi (1.20.2) to analyse data from Illumina MethylEPIC 850k beadchip. I have 24 samples on 3 arrays.  I am pretty new to this kinf of analysis, and R in general, so my question may seem really naïve, but I would really appreciate your help.  When I run qcReport, I ha ...
minfi illumina densityplot methylationepic written 2.3 years ago by annabelle.congras10

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