Question: Prostar (query on GO analysis)
0
gravatar for laural710
10 months ago by
laural7100
laural7100 wrote:

Many thanks in advance for any help with this because i'm stratching my head. I am using Prostar for differential expression of shotgun proteomics data. As part of the process, I reduce the data down to FDR <1%, p-value <0.5 equivalent to a set of genes that are differentially expressed between my two conditions with no NA values at this point. 

My issue is that when i move to the next step which is GO analysis, i get the error "Warning: Error in <-: NAs are not allowed in subscripted assignments" which i'm not sure what it means cause there should be no NAs in the differentially expressed dataset. GO analysis uses the package ClusterProfiler which is present in my packages so i dont thingk that is what is wrong. 

I've updated the packages, R, R-studio, i'm tried to use different datasets, but i am still getting this message. This is extremely new to me and i would appreciate any advice or perhaps a fresh perspective. 

 

 

clusterprofiler prostar dapar • 276 views
ADD COMMENTlink modified 10 months ago by Samuel Wieczorek0 • written 10 months ago by laural7100

It would help if you could provide the code that it is returning this error, and even more if we had the data or some sample data that could reproduce the error.

ADD REPLYlink written 10 months ago by Lluís Revilla Sancho460

Hi Lluis, I'm not sure i can provide an example or dataset as Prostar is a shiny gui interface to numerous proteomics packages. The portion i am having issues with is the GO analysis which interfaces to the clusterProfiler package.

At the moment, i can't even run the Prostar GUI as i am getting this error "Warning in Sys.setlocale("LC_ALL", "en_GB.UTF-8") :OS reports request to set locale to "en_GB.UTF-8" cannot be honored"  and am trying to problem solve this issue. What is annoying is that this was working fine last week before i updated some packages. 

ADD REPLYlink written 10 months ago by laural7100
Answer: Prostar (query on GO analysis)
0
gravatar for Samuel Wieczorek
10 months ago by
France
Samuel Wieczorek0 wrote:

Hi

I am the developer of the Prostar package.

Can you send a print screen of the logSession tab once the differential analysis has been saved ?

And, if possible, the MSnset or Excel file which correspond to your dataset (using the export tool in Prostar) ?

ADD COMMENTlink written 10 months ago by Samuel Wieczorek0
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