User: stu111538

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stu1115380
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Posts by stu111538

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Comment: C: WGCNA: 1) low soft thresholding power, 2) large modules, 3) best correlation for
... Thank you for your comments and support! I will check whether there are global drivers of expression. It might just be that those drivers are exactly the variables I am interested in. ...
written 29 days ago by stu1115380
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WGCNA: 1) low soft thresholding power, 2) large modules, 3) best correlation for different types of trait variables
... Hello, I performed WGCNA on RNA-Seq data of 55 samples and used the code exactly as provided at the WGCNA website for the network analysis of the female mice data. There are three issues I am not sure about: 1) According to the tutorial recommendations I would need to choose a soft thresholding pow ...
wgcna written 8 weeks ago by stu1115380 • updated 8 weeks ago by Peter Langfelder2.3k
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Comment: A: U-shape of p-value histograms is removed by filtering for genes that have >5 cou
... Yes, this answers my question, thank you Michael! Sorry, I was not aware that independent filtering only has influence on the adjusted p-values. ...
written 10 months ago by stu1115380
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U-shape of p-value histograms is removed by filtering for genes that have >5 counts in >10% of samples before applying DESeq2 analysis
... Hi, I used DESeq2 for several differential expression analyses for paired patient samples (sample sizes in the range of 6 to 34 patients). The unadjusted p-values (with applying independentFiltering = TRUE) of the DESeq2 analyses (both Wald test and time series experiments using LRT) **always** show ...
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Comment: C: BSgenomeForge error in .TwoBits_export
... ok, thank you very much! Then, I will wait until Monday and try to install the fixed BSgenome. ...
written 2.2 years ago by stu1115380
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Answer: A: BSgenomeForge error in .TwoBits_export
... In the package destdir 'BSgenome.Hsapiens.NCBI.GRCh38.p11' there is a file called R/zzz.R. This is its content, maybe it helps ### ### .pkgname <- "BSgenome.Hsapiens.NCBI.GRCh38.p11" .seqnames <- NULL .circ_seqs <- "NC_012920.1" .mseqnames <- NULL .onLoad <- function(libname, pk ...
written 2.2 years ago by stu1115380
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Answer: A: BSgenomeForge error in .TwoBits_export
... Hi Herve, sorry, for the confusion! I just added the RRBS-spike sequences for internal control of conversion rate. I also used those sequences for the alignment, that is why I thought it might be better to inlcude them in the GRCh38.p11 reference for BSgenome (I wanted to prevent error messages bec ...
written 2.2 years ago by stu1115380
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BSgenomeForge error in .TwoBits_export
... Hello, Using "forgeBSgenomeDataPkg" I get an error I cannot solve. The problem seems to be to create the twobit file. I have write permission in the destdir and enough disc space on my drive. The sequence data are located in a directory mounted from a linux-server, but I think this is not the probl ...
bsgenome forge twobits_export written 2.2 years ago by stu1115380 • updated 2.2 years ago by Hervé Pagès ♦♦ 14k

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