Question: mgsa vignette gives an error with the full yeast GAF
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gravatar for nmcglincy
4.9 years ago by
nmcglincy0
United States
nmcglincy0 wrote:

Dear All,

I was trying to extend the analysis outlined in the mgsa vignette by using the full yeast GAF instead of the provided example. However, the mgsa() command failed, giving me an error I did not understand.

My code, including the results of traceback() and session_info():

# VINGETTE FOR MGSA
library(mgsa)
data("example")
example_go
example_o
# 
# FIT THE MODEL
set.seed(0)
fit = mgsa(example_o, example_go)
fit
plot(fit)
# 
# READING FULL GAF FILE
# DOWNLOADED FROM http://geneontology.org/page/download-annotations ON 20150115 the unzipped.
#
go.full = readGAF(filename = "gene_association.sgd")
go.full
fit.full = mgsa(o = example_o, 
                sets = go.full)
# 
# Error in matrix(raw$marg, ncol = restarts) : 
#   'data' must be of a vector type, was 'NULL'
# In addition: Warning message:
#   In mgsa(o = example_o, sets = go.full) :
#   Specified observation contains 43 unmapple items. Excluded them from calculation.
# 
traceback()
# 4: matrix(raw$marg, ncol = restarts)
# 3: mgsa.wrapper(items, sets@sets, sets@numberOfItems, alpha, beta, 
#                 p, steps, restarts, threads)
# 2: mgsa(o = example_o, sets = go.full)
# 1: mgsa(o = example_o, sets = go.full)
# 
library(devtools)
devtools::session_info()
# 
# Session info-----------------------------------------------------------------------------------------------
#   setting  value                       
# version  R version 3.1.2 (2014-10-31)
# system   x86_64, darwin13.4.0        
# ui       RStudio (0.98.1091)         
# language (EN)                        
# collate  en_US.UTF-8                 
# tz       America/Los_Angeles         
# 
# Packages---------------------------------------------------------------------------------------------------
#   package       * version   date       source        
# AnnotationDbi * 1.28.1    2014-10-28 Bioconductor  
# Biobase       * 2.26.0    2014-10-14 Bioconductor  
# BiocGenerics  * 0.12.1    2014-11-14 Bioconductor  
# bitops          1.0.6     2013-08-17 CRAN (R 3.1.0)
# caTools         1.17.1    2014-09-10 CRAN (R 3.1.1)
# DBI           * 0.3.1     2014-09-24 CRAN (R 3.1.1)
# devtools      * 1.6.1     2014-10-07 CRAN (R 3.1.1)
# gdata           2.13.3    2014-04-06 CRAN (R 3.1.0)
# GenomeInfoDb  * 1.2.4     2014-12-19 Bioconductor  
# GO.db         * 3.0.0     2014-09-26 Bioconductor  
# gplots        * 2.16.0    2015-01-07 CRAN (R 3.1.2)
# gtools          3.4.1     2014-05-28 CRAN (R 3.1.0)
# IRanges       * 2.0.1     2014-12-12 Bioconductor  
# KernSmooth      2.23.13   2014-09-14 CRAN (R 3.1.2)
# mgsa          * 1.14.2    2014-11-08 Bioconductor  
# RSQLite       * 1.0.0     2014-10-25 CRAN (R 3.1.2)
# rstudio         0.98.1091 2015-01-06 local         
# rstudioapi      0.2       2014-12-31 CRAN (R 3.1.2)
# S4Vectors     * 0.4.0     2014-10-14 Bioconductor  

Any suggestion would be much appreciated!

Best,

Nick

---

Nicholas McGlincy Ph.D.

 

Ingolia Lab

 

Department of Molecular & Cell Biology

University of California, Berkeley

16 Barker Hall # 3202

Berkeley, CA 94720-3202

USA

 

http://www.ingolia-lab.org/

Phone (lab): +1 510 664 7069

Phone (cel): +1 859 489 1926

Email: mcglincy@berkeley.edu

 
go yeast mgsa software error • 797 views
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