Question

Running GO analysis via Prostar

1

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lolli.langan ▴ 20

@lollilangan-15141

Last seen 5.9 years ago

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.

prostar proteomics rforproteomics annotationforge • 1.3k views

ADD COMMENT • link updated 5.9 years ago by Samuel Wieczorek ▴ 10 • written 5.9 years ago by lolli.langan ▴ 20

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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 REPLY • link 5.9 years ago James W. MacDonald 65k

score 0 · Answer 1 · 2018-06-01

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Samuel Wieczorek ▴ 10

@samuel-wieczorek-8454

Last seen 5 weeks ago

France

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 COMMENT • link 5.9 years ago Samuel Wieczorek ▴ 10

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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 REPLY • link 5.9 years ago lolli.langan ▴ 20