User: sarka.vorackova

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Posts by sarka.vorackova

<prev • 9 results • page 1 of 1 • next >
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Comment: C: Analysis of DNA hydroxymethylation
... Hi Yuan Tian, thanks for such quick answer!! I sure noticed that there is a paragraph in ChAMP vignette but I am not sure if it is suitable for my data. I have 6 Sample Groups (samples with different mutations and normal) and for each sample I have BS and oxBS data. So first I need to asses BS-oxB ...
written 23 months ago by sarka.vorackova0
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Analysis of DNA hydroxymethylation
... Hi, I have a set of BS and oxBS treated samples from EPICarray and would like to analyze them using a R package. I found there are oxyBS and oxBS-MLE packages but I am struggling with their implementation to the analysis itself. For the methylation analysis I use the ChAMP and minfi packages so can ...
champ minf oxybs oxbs-mle written 23 months ago by sarka.vorackova0 • updated 23 months ago by Yuan Tian80
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Answer: A: New version of ChAMP can not proceed through champ.DMP
... Dear Yuan Tian, thank you for the quick answer! I unfortunatelly don't have the previous output of dmps because I had only testing set of samples to see if it works on my computer anyway I loaded and normalized the data through default methods (ChAMP, BMIQ). For the current analysis I am imputting ...
written 2.0 years ago by sarka.vorackova0
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New version of ChAMP can not proceed through champ.DMP
... Hi, I recently got the new version of ChAMP 2.8.9 and now I can not proceed through champ.DMP, an error now occures that did not show up when I was using the previous version 2.8.7. champ.DMP runs without problem until the annotation section. myDMP <- champ.DMP(arraytype = "EPIC") #now it find ...
champ written 2.0 years ago by sarka.vorackova0
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Comment: C: ChAMP filter removing good samples from different batch of EPIC arrays.
... Thank you Yuan Tian, I just installed the new version and the data loading works perfectly! Best, Sarka   ...
written 2.0 years ago by sarka.vorackova0
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Comment: C: ChAMP filter removing good samples from different batch of EPIC arrays.
... Great, thanks for answers and everything!! Sarka ...
written 2.0 years ago by sarka.vorackova0
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Answer: A: ChAMP filter removing good samples from different batch of EPIC arrays.
... Great, thanks for answers and everything!! Sarka ...
written 2.0 years ago by sarka.vorackova0
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ChAMP filter removing good samples from different batch of EPIC arrays.
... Hi, I have a problem analysing EPIC arrays with ChAMP. I have a set of 7 arrays - one part of arrays was done during November 2016-January 2017 (4 arrays), second part was done in June 2017. When I analysed the first and second portion of arrays separately, everything seems ok in both cases, all the ...
minfi champ written 2.0 years ago by sarka.vorackova0 • updated 2.0 years ago by Yuan Tian80
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doRNG installation failure
... Hi, I would like to use the minfi package, so I insltalled it and all went well except the package doRNG which fails to install. I tried to download the package and istall it from computer but it also failed. Please can anyone help? I am a new user of R and I do not have many experience. Tank you! ...
minfi error package installation dorng written 2.4 years ago by sarka.vorackova0

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