## User: sven.schenk

sven.schenk10
Reputation:
10
Status:
New User
Location:
Vienna
Last seen:
2 months ago
Joined:
1 year, 1 month ago
Email:
s**********@univie.ac.at

#### Posts by sven.schenk

<prev • 16 results • page 1 of 2 • next >
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... Hi, thanks a lot for clarifying this. Sven ...
written 3 months ago by sven.schenk10
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... Hello, I am analysing a RNA-Seq experiment using DESeq2 trying to understand the different log2Fold shrinking algorithms available in DESeq2. After reading the documentation I understood that setting betaPrior=TRUE when calling DESeq would use the "normal" log2Fold shrinking as it was used as d ...
written 3 months ago by sven.schenk10 • updated 3 months ago by Michael Love24k
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... We also tried using DESeq on proteomics data, and this gave extrmely high numbers of rejections (of the null), which didnt 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 10 months ago by sven.schenk10
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... Thanks, I actually saw that betaPrior is now set to FALSE, but I ignored it as I thought Id 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 12 months ago by sven.schenk10
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... 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 ...
written 12 months ago by sven.schenk10
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... 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 12 months ago by sven.schenk10
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... 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 12 months ago by sven.schenk10
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... Thanks, let`s see if it helps. ...
written 12 months ago by sven.schenk10
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... 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 ...
written 12 months ago by sven.schenk10 • updated 12 months ago by Michael Love24k
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... 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 12 months ago by sven.schenk10

#### Latest awards to sven.schenk

Autobiographer 12 months ago, has more than 80 characters in the information field of the user's profile.

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