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Question: biocLITE annotation Rstudio
0
gravatar for jemaatita
3 months ago by
jemaatita0
jemaatita0 wrote:

Hello! I was working on this annotation function for GDS4523

and I used the following function but it came as error

annotation(eset)  <- "HG-U133_Plus_2" 
biocLite("HG-U133_Plus_2.db") 
library(HG-U133_Plus_2.db)

Warning message:
package ‘HG-U133_Plus_2.db’ is not available (for R version 3.2.2) 
> library(HG-U133_Plus_2.db)
Error in library(HG - U133_Plus_2.db) : 'package' must be of length 1

So i don't know how to fix this as I need to finish the gene filtering before monday, it would be great if anyone can help me solving this

ADD COMMENTlink modified 3 months ago by James W. MacDonald45k • written 3 months ago by jemaatita0
0
gravatar for James W. MacDonald
3 months ago by
United States
James W. MacDonald45k wrote:

The annotation packages are all lower case and contain no symbols (dashes, underscores, etc) so you want

biocLite("hgu133plus2.db")
library(hgu133plus2.db)
ADD COMMENTlink modified 3 months ago • written 3 months ago by James W. MacDonald45k

Tried it... but it say after running biocLite(hgu133plus2.db) and install everything there is a warning massage:

Warning messages:
1: running command '"C:/PROGRA~1/R/R-32~1.2/bin/x64/R" CMD INSTALL -l "C:\Users\Jedi\Documents\R\win-library\3.2" C:\Users\Jedi\AppData\Local\Temp\RtmpWIppjW/downloaded_packages/org.Hs.eg.db_3.2.3.tar.gz' had status 1 
2: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘org.Hs.eg.db’ had non-zero exit status
3: running command '"C:/PROGRA~1/R/R-32~1.2/bin/x64/R" CMD INSTALL -l "C:\Users\Jedi\Documents\R\win-library\3.2" C:\Users\Jedi\AppData\Local\Temp\RtmpWIppjW/downloaded_packages/hgu133plus2.db_3.2.2.tar.gz' had status 1 
4: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘hgu133plus2.db’ had non-zero exit status

> library(hgu133plus2.db)
Error in library(hgu133plus2.db) : 
  there is no package called ‘hgu133plus2.db’

ADD REPLYlink modified 3 months ago • written 3 months ago by jemaatita0

Well, the error is pretty clear as to what happened - the package didn't get installed. Unfortunately it's not clear why. You might try again and see if it works.

ADD REPLYlink written 3 months ago by James W. MacDonald45k

It looks like it is failing because the dependency package "org.Hs.eg.db" failed to install.  Could you please try running  `biocLite("org.Hs.eg.db")`  and provide the output if it does not work correctly?  Also could you please provided your `sessionInfo()`

ADD REPLYlink written 3 months ago by shepherl ♦♦ 510
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