User: rea

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rea • 10
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Posts by rea

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Answer: A: Failure to update BiocGenerics in Ubuntu 17.10 from 0.22.1 to 0.23 and higher
... I couldn't understand the first proposal of solution. I solved the problem by updating R to the latest version by following the instructions at https://cran.r-project.org/bin/linux/ubuntu and by installing the Bioconductor package.       ...
written 19 months ago by rea • 10
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Answer: A: Failure to update BiocGenerics in Ubuntu 17.10 from 0.22.1 to 0.23 and higher
... What is the effect of R --vanilla -e "BiocInstaller::biocLite("BiocGenerics") It does not seem to open an R session. What should I type in? source("https://bioconductor.org/biocLite.R") biocLite("BiocGenerics")   or source("https://bioconductor.org/biocLite.R") biocLite("BiocUpgrade")   ...
written 19 months ago by rea • 10
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Comment: C: Failure to update BiocGenerics in Ubuntu 17.10 from 0.22.1 to 0.23 and higher
... Here's the output installing *source* package ‘BiocGenerics’ ... ** R ** inst ** preparing package for lazy loading Creating a new generic function for ‘append’ in package ‘BiocGenerics’ Creating a new generic function for ‘as.data.frame’ in package ‘BiocGenerics’ Creating a new generic function f ...
written 19 months ago by rea • 10
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Failure to update BiocGenerics in Ubuntu 17.10 from 0.22.1 to 0.23 and higher
... Dear All, I am unable to update package BiocGenerics which is required to install BSgenome. I tried: source("https://bioconductor.org/biocLite.R") biocLite("BiocGenerics") and got the following error message: BioC_mirror: https://bioconductor.org Using Bioconductor 3.6 (BiocInstaller 1.28.0), ...
biocgenerics written 19 months ago by rea • 10
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retrieve genes from mroast in limma
... Do you know how to retrieve the genes corresponding to the proportions of up-/down-regulated genes reported in the mroast() output withinthe limma package? Documentation mentions thresholds on z. However, how could you compute the mentioned z?   ...
limma written 2.8 years ago by rea • 10 • updated 2.8 years ago by Gordon Smyth ♦ 38k
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dexseq_count.py in shell script
... To use DEXSeq,which is the effective way to execute the Python dexseq_count.py script in a shell script without receiving errors such as 'import.im6: unable to open X server `' @ error/import.c/ImportImageCommand/368'? Thank you foe any suggestion. ...
py written 2.9 years ago by rea • 10
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interaction formulas without replicates
... I refer to section 3.3.2 on nested interaction formulas in the edgeR user guide. I wonder if the coefficient TreatDrug.Time.1h provides the logFC and associated FDR corresponding to (drug.1h-drug.0h)-(placebo.1h-placebo.0h). Is this interpretation correct? Does it make sense to use nested interact ...
cancer written 3.0 years ago by rea • 10 • updated 3.0 years ago by Aaron Lun • 24k

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