User: sven.schenk

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sven.schenk10
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Vienna
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Posts by sven.schenk

<prev • 14 results • page 1 of 2 • next >
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Answer: A: DESeq2 with proteomics data
... We also tried using DESeq on proteomics data, and this gave extrmely high numbers of rejections (of the null), which didn`t seem to be realistic. The difference between RNASeq and proteomics data is that protein intensities are continuous data and not simple counts as are RNASeq data. This, I guess ...
written 17 days ago by sven.schenk10
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Comment: C: very different DESeq2 results between two versions
... Thanks, I actually saw that betaPrior is now set to FALSE, but I ignored it as I thought I`d anyway never used it, but if it was TRUE by default. My mistake. When I now run DESeq with betaPrior=TRUE and get the same result as before (Aug 17), which should give  the result same as if I had used the ...
written 8 weeks ago by sven.schenk10
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very different DESeq2 results between two versions
... Hi, last year I ran DESeq2 on RNASeq data comparing treated vs untreated cells. When I initially ran DESeq2 I found that I had rather low log2FC and a kind of high variation. However, I now re-ran DESeq2 on the same data with the same script ddsFullCountTable <- DESeqDataSetFromMatrix(countDat ...
rnaseq deseq2 written 8 weeks ago by sven.schenk10
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Comment: C: Defining subsets for FDR correction
... ok, that makes sense so nothing that comes out of DESeq (apart from baseMean) can be used. But I was thinking if baseMean is independent so should be SD(baseMean) this would also most directly account for my varioation issue.   ...
written 8 weeks ago by sven.schenk10
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Comment: C: Defining subsets for FDR correction
... ok, I guessed as much. so that would mean I should generally not filter like this: interestingGenes<-subset(input, abs(lfcSE*sqrt(3)/log2FoldChange)<=1) but rather use use something involving baseMean,but how would I find an unbiased way to define a cut off for my subset? Could I use baseM ...
written 9 weeks ago by sven.schenk10
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Comment: C: Defining subsets for FDR correction
... Thanks, let`s see if it helps. ...
written 9 weeks ago by sven.schenk10
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Defining subsets for FDR correction
... Hello, I have rather general question concering FDR/adjusted pvalues. I did an RNASeq experiment (treated vs untreated cells), and analysed the data with DESeq. There I found that I had only very few transcripts passing the FDR cut off at 0.1, which I assumed to be because I have rather low effect ...
deseq2 fdr ihw written 9 weeks ago by sven.schenk10 • updated 9 weeks ago by Michael Love19k
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Comment: C: comparing two GOstats result lists
... Hi thanks for your answer. Yes, I think roast would do exactly what I'd want, but for that I'd have to have replicates which I don't have. I have only the Counts from one enrichment analysis the Counts from the second one which I want to compare to each other. I then found that I could use geneSet ...
written 9 weeks ago by sven.schenk10
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comparing two GOstats result lists
... Hi, I am trying to compare two result lists from GOstats. The reason for doing this is that I did a proteomics experiment in which we established a new sample preparation protocol and I now want to kind of show that with this new method we do not enrich/deplete for certain proteins/protein function ...
gostats statistics written 10 weeks ago by sven.schenk10 • updated 10 weeks ago by James W. MacDonald47k
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Comment: C: GO Stats results contain GO terms NOT present in the gene universe
... hi,   thanks for your answer. i came to the same conclusion, when checking what`s happening during building the GOallframe - in this I have something like 4700 Go terms insteadt of 2472 in my input list. so it was indeed a misunderstanding how GOstats works. thanks again for the answer and the ad ...
written 12 weeks ago by sven.schenk10

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