Question: Running GO analysis via Prostar
1
gravatar for lolli.langan
12 months ago by
lolli.langan20
lolli.langan20 wrote:

I recently upgraded to the new Prostar (for proteomics analysis).

Within the gene ontology analysis, it was possible to use genome wide annotation packages you had already installed or at least they were available/searchable during analysis to link up GO numbers etc.

This does not appear to be the case now and i wonder is it a glitch or is it due to recent upgrades to R and some of the connecting packages have dropped a link or something?

My question is how do i contact the package developers to query this or is there something i can do as a novice (comparatively) user? 

Any help would be much appreciated. 

ADD COMMENTlink modified 12 months ago by Samuel Wieczorek0 • written 12 months ago by lolli.langan20

The maintainer of the package is supposed to monitor this support site for questions about their package, so maybe you just have to wait. Otherwise, see the output from

library(prostar)

packageDescription("prostar")$Maintainer
ADD REPLYlink written 12 months ago by James W. MacDonald50k
Answer: Running GO analysis via Prostar
0
gravatar for Samuel Wieczorek
12 months ago by
France
Samuel Wieczorek0 wrote:

Hi, I am the developer of the package Prostar.

Due to the update of R version, You should reinstall the annotation packages you need. This can be done with the following commands (in this example, the package is org.Hs.eg.db

source("https://bioconductor.org/biocLite.R")

biocLite("org.Hs.eg.db")

 

Install all the annotation packages you have to use

 

Let me know if it solves your problem

 

Best

Sam

ADD COMMENTlink written 12 months ago by Samuel Wieczorek0

Hi Sam

I'm having two very differnt problems dependent on which system i work on. In the first instance, i have ran the analysis on my personal MAC and while the biocLite package is recognised via the Prostar gui, the annotation package i have built via the annotationForge package (my organism is currently not availble via bioconductor) is not recognised despite having similiar nomenclature and data available in both. 

In contrast, when running the analysis via my windows work computer, neither the bioclite db nor my own personal annotation db are recognised. 

I recognise this may be two completely different problems related to the different systems, but i do find it weird that on my MAC, i cannot get it to recognise the annotation forge built db (which is visible and loadable in the R console). Any help with this would be much appreciated.

Best

Laura

ADD REPLYlink written 12 months ago by lolli.langan20
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