User: theodore.georgomanolis

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Posts by theodore.georgomanolis

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Is it possible to use Rnbeads with WGBS data from epigenetics roadmap/ucsc data
... Dear all, I have a three files from epigenetics roadmap that have already been analyzed and I got the bigwig files with the already calculated percentage of the methylation. Is it possible to use those files perform differential analysis of the methylated sites using Rnbeads? If so, is it possible ...
rnbeads wgbs written 13 days ago by theodore.georgomanolis0
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Comment: C: FourCseq: getZScores errors, first case 6 digenerated cutterm second case 4 base
... Should I send a new question with a DESeq2 tag? ...
written 14 months ago by theodore.georgomanolis0
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Comment: C: FourCseq, rawRanges Description
... Hi Felix, I will look at them and come back to you. Thank you again for your help ...
written 14 months ago by theodore.georgomanolis0
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FourCseq, rawRanges Description
... Hi Felix once more, I am trying to figure out a few things on the R script and I wandering what the rawRanges holds. I can extract the following items: leftSize rightSize leftValid rightValid mid dist posLeft posRight blind vpChr tooClose lowCounts selectedForF ...
fourcseq written 14 months ago by theodore.georgomanolis0 • updated 14 months ago by felix.klein140
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Answer: A: FourCseq: getZScores errors, first case 6 digenerated cutterm second case 4 base
... Regarding the same set, I encounter another problem while I was  fcf <- getDifferences(fcf, referenceCondition="0min") the output was > fcf <- getDifferences(fcf, + referenceCondition="0min") [1] SAM_ApoI Levels: SAM_ApoI found already estimated dispersions, replacing these gene-wise d ...
written 14 months ago by theodore.georgomanolis0
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Comment: C: FourCseq: getZScores errors, first case 6 digenerated cutterm second case 4 base
... Hey Felix, SO, I tried to mix the data set with an other dataset and I could lower significantly the minCount to 100, which is reasonable. Scatter plot looks the same when I am comparing the same datasets, but I was wondering if I will get more false "significant" contacts. the QQ plots are lookin ...
written 14 months ago by theodore.georgomanolis0
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Answer: A: FourCseq: getZScores errors, first case 6 digenerated cutterm second case 4 base
... Hi, Felix here is the scatterplot of the two replicates https://drive.google.com/open?id=0ByX6rNLnP_9qbTNtQWIya244Q1U https://drive.google.com/open?id=0ByX6rNLnP_9qemc1REM2YmRJVTQ So, I change the minCount on the getZscore function and I fount that the minCount in my case is 2390 > fcf<-ge ...
written 14 months ago by theodore.georgomanolis0
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Answer: A: FourCseq: mixed amount of replication/samples
... Great, thank you ...
written 14 months ago by theodore.georgomanolis0
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FourCseq: mixed amount of replication/samples
... This is a simple question but let's say that I got the following samples Condition1_rep1 Condition1_rep2 Condition1_rep3 Condition2_rep1 Condition2_rep2 Condition3_rep1 Condition3_rep2 Condition3_rep3 Condition3_rep4 Your code on the DataFrame function for creating a data frame (colData) needs ...
fourcseq written 14 months ago by theodore.georgomanolis0
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FourCseq: getZScores errors, first case 6 digenerated cutterm second case 4 base cutter
... Hi Felix, Hi to all, I am getting trouble at the getZscores step First situation > fcf<-getZScores(fc19) [1] "SAMD4A_ApoI" gene-wise dispersion estimates mean-dispersion relationship -- note: fitType='parametric', but the dispersion trend was not well captured by the function: y = a/x + ...
fourcseq written 14 months ago by theodore.georgomanolis0

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