Warning with the example of GSEA
2
0
Entering edit mode
@a287dbc4
Last seen 4 days ago
France

I try to run the example of fgsea package with R version 4.0.2 :

data(examplePathways)
data(exampleRanks)
typeof(examplePathways)
fgseaRes <- fgsea(pathways = examplePathways, 
                  stats = exampleRanks,
                  minSize=15,
                  maxSize=500,
                  nperm=10000)

I got this warning and I don't know how to deal with that

Warning messages:
1: In fgsea(pathways = examplePathways, stats = exampleRanks, minSize = 15,  :
  You are trying to run fgseaSimple. It is recommended to use fgseaMultilevel. To run fgseaMultilevel, you need to remove the nperm argument in the fgsea function call.
2: In serialize(data, node$con) :
  'package:stats' peut-être indisponible lors du chargement
3: In serialize(data, node$con) :
  'package:stats' peut-être indisponible lors du chargement
4: In serialize(data, node$con) :
  'package:stats' peut-être indisponible lors du chargement
5: In serialize(data, node$con) :
  'package:stats' peut-être indisponible lors du chargement
6: In serialize(data, node$con) :
  'package:stats' peut-être indisponible lors du chargement
7: In serialize(data, node$con) :
  'package:stats' peut-être indisponible lors du chargement

I use this to install the package :

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("fgsea")
fgsea fgse • 141 views
ADD COMMENT
1
Entering edit mode

Hi, I think that nperm is too high. Can you re-run without setting any value for nperm?

Kevin

ADD REPLY
2
Entering edit mode
assaron ▴ 200
@assaron
Last seen 5 days ago
St Petersburg

There are two warnings.

You are trying to run fgseaSimple can be solved by removing nperm parameter at all. The nperm parameter is deprecated, and generally shouldn't be used. Also, where this example is coming from?

The second warning about serialize(data, node$con) is related to parallel execution. Not sure what exactly happens, but a workaround is to run fgsea in single-threaded mode, for example by specifying nproc=1 as a parameter.

ADD COMMENT
0
Entering edit mode
@a287dbc4
Last seen 4 days ago
France

Thank you for your help ! I did this and it is work well !

data(examplePathways)
data(exampleRanks)
typeof(examplePathways)
fgseaRes <- fgsea(pathways = examplePathways, 
                  stats = exampleRanks,
                  minSize=15,
                  maxSize=500,
                  nproc=1, 
                  eps = 0)

I foun this example here : https://bioconductor.org/packages/release/bioc/vignettes/fgsea/inst/doc/fgsea-tutorial.html

ADD COMMENT

Login before adding your answer.

Traffic: 430 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6