User: Fischer-philipp

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Posts by Fischer-philipp

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Answer: A: update all/some/none how to set default to "update all"
... There is a way using the package `pacman`.and its function `p_load`. This should to what you want. ``` p_load("Biostrings") ``` The following code is usefull if you have to run lots of packages. ``` load.libs <- c("Biostrings") #and some more packages if (!require("pacman")) install.package ...
written 4 weeks ago by Fischer-philipp0
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Answer: A: edgeR /DESeq2 normalization for differential expression in RNA-seq blood samples
... Yes I think so normalization with DESeq2 and edgeR does take into account the library composition (meaning the composition between samples). In DESeq2 the normalization is done via a sclaing factor which is calculated via the geometric mean. The geometric mean does not emphasize on "outliers". Furt ...
written 5 weeks ago by Fischer-philipp0
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Comment: C: glm.fit problem with maSigPro
... Could you post your code? ...
written 5 weeks ago by Fischer-philipp0
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Comment: C: DESeq2: 5 Conditions (B vs C) vs (D vs B)
... Thank you for your answer. Just for confirmation: The code would be like this (with lfcThreshold = 0). And the results would just be a list. ``` m1 <- results(dds_f, contrast = c(0, 0, 1, -1, 0)) #B vs C m2 <- results(dds_f, contrast = c(0, 0, -1, 0, 1)) #D vs B rn.m1 <- rownames(m1)[m1$ ...
written 5 weeks ago by Fischer-philipp0
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DESeq2: 5 Conditions (B vs C) vs (D vs B)
... DESeq2: 5 Conditions (B vs C) vs (D vs B) Consider a setup with 5 Conditions A-E, where E is the untreated condition and hence the reference label. I want to know which genes are upregulated in B vs C but are downregulated in D vs B. All samples should be compared to E (the untreated condition) ...
deseq2 contrast ratio of ratio written 5 weeks ago by Fischer-philipp0 • updated 5 weeks ago by Michael Love22k
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Typo / Mistyped in rWikipathways - 4. Pathway Analysis? (GSEA) / NES <-1 instead of NES < 1 for downregulated genes
... Hey everyone, I was reading the documentation of rWikipathways( check link below) when I think I encountered a typo.  https://bioconductor.org/packages/release/bioc/vignettes/rWikiPathways/inst/doc/Pathway-Analysis.html After running GSEA() one is to distinguish which pathways are enriched for up ...

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