search for: deseq2

Hi , I am trying to open vignette DESeq2 but getting below error: > vignette("DESeq2") > START /usr/bin/evince "/usr/lib64/R/library/DESeq2/doc/DESeq2.pdf" Cannot parse arguments: Cannot open display: xdg-open: no method available for opening '/usr/lib64/R/library/DESeq2/doc/DESeq2.pdf' -- *Yogesh Gupt...

There are two line 216 and 218 Three development stages 5 WEEK (5W), 7W, 9W. Three tissue: Ca, Co, Pa each with 2 biological replicate. With two biological replicate. I want to do differential gene expression analysis using DESeq2 so I tried these codes after reading about DESeq2: ,my aim is to do the pairwise comparison. how to make colData and design formula. library("DESeq2") countMatrix = read.table("read_count.22May.2017.new.txt",header=T,sep='\t',check.names=F) head(countMatrix) dim(coun...

...ired at any one time. >> Good practice is to load namespaces as required, using requireNamespace. > > Extensive package dependencies in Bioconductor make it pretty easy to end up with dozen of packages attached or loaded. For instance > > library(GenomicFeatures) > library(DESeq2) > > > length(loadedNamespaces()) > [1] 63 > > length(getLoadedDLLs()) > [1] 41 > > Qin's use case is a shiny app, presumably trying to provide relatively comprehensive access to a particular domain. Even if the app were to load / requireNamespace() (this requires c...

On 04/05/2016 08:44, Martin Maechler wrote: >>>>>> Qin Zhu <qinzhu at outlook.com> >>>>>> on Mon, 2 May 2016 16:19:44 -0400 writes: > > > Hi, > > I?m working on a Shiny app for statistical analysis. I ran into this "maximal number of DLLs reached" issue recently because my app requires importing many other packages.

...ore than a few are required at any one time. > Good practice is to load namespaces as required, using requireNamespace. Extensive package dependencies in Bioconductor make it pretty easy to end up with dozen of packages attached or loaded. For instance library(GenomicFeatures) library(DESeq2) > length(loadedNamespaces()) [1] 63 > length(getLoadedDLLs()) [1] 41 Qin's use case is a shiny app, presumably trying to provide relatively comprehensive access to a particular domain. Even if the app were to load / requireNamespace() (this requires considerable programming discip...

...ractice is to load namespaces as required, using requireNamespace. >> >> Extensive package dependencies in Bioconductor make it pretty easy to end up with dozen of packages attached or loaded. For instance >> >> library(GenomicFeatures) >> library(DESeq2) >> >> > length(loadedNamespaces()) >> [1] 63 >> > length(getLoadedDLLs()) >> [1] 41 >> >> Qin's use case is a shiny app, presumably trying to provide relatively comprehensive access to a particular domain. Even if th...