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Question: biocLITE annotation Rstudio
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14 months ago by
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

modified 14 months ago by James W. MacDonald48k • written 14 months ago by jemaatita0
0
14 months ago by
United States
James W. MacDonald48k 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 14 months ago • written 14 months ago by James W. MacDonald48k

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 14 months ago • written 14 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 14 months ago by James W. MacDonald48k

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 14 months ago by shepherl ♦♦ 830