User: deut13

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deut1350
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Germany
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8 months, 2 weeks ago
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2 years, 3 months ago
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d*****@gmail.com

Posts by deut13

<prev • 15 results • page 1 of 2 • next >
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Comment: C: Error in GRanges: could not find symbol "recursive" in environment of the generi
... Thank you all! I had searched online but missed the other post. After reinstalling from source the issue seems solved. (Before I had to remove the installed packages and then also manually delete what remained in the library folders - without this it was giving a problem in copying the .dll files ...
written 8 months ago by deut1350
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Error in GRanges: could not find symbol "recursive" in environment of the generic function
... Hi all, I would be grateful for help on the following issue. When running the function annotatePeakInBatch from package ChIPpeakAnno I get the following error: Error in c(<S4 object of class "GRanges">, <S4 object of class "GRanges">, : could not find symbol "recursive" in enviro ...
chippeakanno granges written 8 months ago by deut1350 • updated 8 months ago by davide.porcellato10
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Comment: C: Question: DESeq2 - factor base level changes LFCs -- hoping to understand this b
... Thanks for the clarification! ...
written 18 months ago by deut1350
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Comment: C: Question: DESeq2 - factor base level changes LFCs -- hoping to understand this b
... Sorry, I meant to write DESeq2 1.8.1 - I have to say I have not (yet) tried with the current 1.12.3 ...
written 18 months ago by deut1350
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Comment: C: Question: DESeq2 - factor base level changes LFCs -- hoping to understand this b
... In R 1.8.1 I have done a small test for a design with no interactions of the type ~line+treatment, where line has 4 different levels. I have noticed (small) differences in the estimated pvalues and adjusted pvalues if I change names of the levels for "line" factor (so that the first level in alphab ...
written 18 months ago by deut1350
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Comment: C: How does DESeq2 handle zero counts in one condition?
... genes with for example all zeros in control condition (the denominator), don't get the same MLE FC, so I guess this depends also on the values of the numerator?   ...
written 19 months ago by deut1350
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Comment: C: How does DESeq2 handle zero counts in one condition?
... does the same hold when using betaprior=FALSE? thanks ...
written 19 months ago by deut1350
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Comment: C: Biclustering Normalizing by Row in Heatmap of DESeq2
... It is a good argument. I was thinking of finding genes with similar 'shape', so that in a case like mat <- matrix(c(1,1,1,10,10,10,10,10,10,100,100,100,rep(1:2,6)),ncol=6,byrow=TRUE) one would separate genes 1-2 from 3-4. ...
written 2.2 years ago by deut1350
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Comment: C: DeSeq2 - hill–shaped histogram of pvalues
... Thanks a lot Bernd for the further suggestions! ...
written 2.2 years ago by deut1350
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Answer: A: Biclustering Normalizing by Row in Heatmap of DESeq2
... Besides removing mean, in some cases it might be useful to use z-scores of the gene profiles in the data matrix: data.t<-t(data) data.scaled<-t(scale(data.t)) If you use heatmap.2 you should input scaled data and use scale="none" as the source code shows that data are scaled after clustering ...
written 2.2 years ago by deut1350

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