biocLITE annotation Rstudio
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jemaatita • 0
@jemaatita-13557
Last seen 4.2 years ago

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

annotation bioclite • 938 views
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@james-w-macdonald-5106
Last seen 13 hours ago
United States

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

biocLite("hgu133plus2.db")
library(hgu133plus2.db)

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

Warning messages:
2: In install.packages(pkgs = doing, lib = lib, ...) :
installation of package ‘org.Hs.eg.db’ had non-zero exit status
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’

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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.

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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()