User: akaever

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akaever30
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Posts by akaever

<prev • 11 results • page 1 of 2 • next >
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Comment: C: Highly differentially expressed genes not found with DESeq2 and default betaPrio
... How can it be explained that for the last row in the spikeIn matrix still a quite high log2FoldChange and low padj are calculated (betaPrior=TRUE)? ...
written 14 months ago by akaever30
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Comment: C: Highly differentially expressed genes not found with DESeq2 and default betaPrio
... We had observed the first and last row of the spikeIn matrix in a real data set. It took some time to figure out what went wrong. In order to demonstrate that the issue is with the single gene and that not the whole data set is the problem, I tested it in the context of a random data set. My experi ...
written 14 months ago by akaever30
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Highly differentially expressed genes not found with DESeq2 and default betaPrior
... Hi, the default DESeq2::DESeq(betaPrior=TRUE) parameter seems to prevent finding single highly significant genes (e.g. inserted into a random data set): library(DESeq2) ex <- makeExampleDESeqDataSet(n = 60000, m = 10) design(ex) <- ~ condition spikeIn <- matrix(as.integer(c(5,0,177,69, ...
deseq2 betaprior written 14 months ago by akaever30 • updated 14 months ago by thomas.siegmund0
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Offline loading of BiocInstaller or depending packages and connection timeout
... When loading the BiocInstaller package or packages which import BiocInstaller (e.g. affy) without internet connection, this results in a long timeout (depends on connection settings) and warns: Warning message: In read.dcf(con) : unable to resolve 'bioconductor.org' The problem is, that packages i ...
affy biocinstaller written 16 months ago by akaever30 • updated 16 months ago by Martin Morgan ♦♦ 20k
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DESeq outlier detection for unbalanced groups
... In case of an unbalanced number of samples per group, the standard DESeq outlier replacement (minReplicatesForReplace=7) can result in drastically reduced p-values. This happens when the trimmed mean replacement leaves out all samples from the smaller group. See the following example: First two val ...
deseq deseq2 outliers written 16 months ago by akaever30 • updated 16 months ago by Michael Love14k
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Comment: C: DESeq results names when using interaction terms
... Pre-calculation using a few rows is a good idea. Thanks for the fast reply! ...
written 16 months ago by akaever30
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Answer: A: DESeq results names when using interaction terms
... Hi, What would be the easiest way to extract the expected resultsNames before calling DESeq(dds) (which may take considerable time)? There seems to be some name conversions between colnames(model.matrix(design(dds), colData(dds))) and resultsNames(dds). ...
written 16 months ago by akaever30
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DESeq results names when using interaction terms
... Hi, I am trying to extract results from a DESeqDataSet object based on a customized contrast list. Depending on whether the design contains an interaction term, the effect/result names change, which makes it quite difficult to extract results in an automatic fashion (e.g. as part of a script or app ...
deseq deseq2 resultsnames written 17 months ago by akaever30
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Unexpected recursive unlist of bplapply (BiocParallel) results when using only one worker
... Hi, bplapply (BiocParallel) seems to return different results when specifying more than one or only one worker core (BPPARAM=MulticoreParam(workers=1)). Of course, using bplapply with only one core doesn't make much sense, but for compatibility the result should be the same. library(BiocParallel ...
biocparallel bplapply written 2.5 years ago by akaever30
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Comment: C: Large disk images of DESeqDataSet / SummarizedExperiment objects when using the
... Thanks for all the replies! It works :-), but I do not fully understand why objects in the .GlobalEnv are not automatically saved in this case. I would have tried design <- as.formula("~ condition", env=emptyenv()) to avoid saving additional objects. ...
written 2.8 years ago by akaever30

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