User: rea
rea • 10
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Posts by rea
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... 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 11 weeks ago by
rea • 10
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... 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 11 weeks ago by
rea • 10
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... 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 11 weeks ago by
rea • 10
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... 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), ...
written 11 weeks ago by
rea • 10
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... 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?
...
written 16 months ago by
rea • 10
• updated 16 months ago by
Gordon Smyth ♦ 33k
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... 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.
...
written 18 months ago by
rea • 10
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... 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 ...
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