categories can not be recognized in Bioconductor/GeneAnswers
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@emiliomastriani-11983
Last seen 4.3 years ago

Hello guys,

I hope that someone of you can help me. 

I just finished my analysis of an Illumina microarray using beadarray. I got all information that I need to start my "concept" investigation using GeneAnswers (it's not the first time that I use it). Something it's not right. It looks that some/many GO categories are missing...

Here is some information:

> x <- geneAnswersBuilder(subsetCL5_Genes, 'org.Hs.eg.db', categoryType='GO', testType='hyperG',  pvalueT=0.1, FDR.correction=TRUE, geneExpressionProfile=CL5)
[1] "geneInput has built in ..."
[1] "annLib and categoryType have built in ..."
[1] "genesInCategory has built in ..."
[1] "Enrichment test is only performed based on annotated genes"
[1] "testType, pvalueT and enrichmentInfo have built in ..."
[1] "geneExpressionProfile has been built in ..."
[1] "GeneAnswers instance has been successfully created!"
> 
> geneAnswersConceptNet(x, color='LogFC', geneLayer=5, output='interactive', showCats=c("GO:0000166"), catTerm=TRUE, geneSymbol=TRUE, catID=TRUE)
Error in geneAnswersConceptNet(x, color = "LogFC", geneLayer = 5, output = "interactive",  : 
  specified categories can not be recognized!

I get the same error loading the following ones: 

GO:0003723GO:0003730GO:0005515GO:0044822GO:0005634GO:0005737GO:0005829GO:0006412GO:0010467GO:0017148GO:0042035

Here is my session:

> sessionInfo()
R version 3.3.2 (2016-10-31)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 14.04.4 LTS

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               LC_TIME=en_US.UTF-8       
 [4] LC_COLLATE=en_US.UTF-8     LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                  LC_ADDRESS=C              
[10] LC_TELEPHONE=C             LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats4    parallel  stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] GeneAnswers_2.16.0        RColorBrewer_1.1-2        Heatplus_2.20.0          
 [4] MASS_7.3-45               RSQLite_1.1-1             annotate_1.52.0          
 [7] XML_3.98-1.5              RCurl_1.95-4.8            bitops_1.0-6             
[10] igraph_1.0.1              GO.db_3.4.0               ggrepel_0.6.5            
[13] beadarray_2.24.0          ggplot2_2.2.0             illuminaHumanv3.db_1.26.0
[16] org.Hs.eg.db_3.4.0        AnnotationDbi_1.36.0      IRanges_2.8.1            
[19] S4Vectors_0.12.1          limma_3.30.7              GEOquery_2.40.0          
[22] Biobase_2.34.0            BiocGenerics_0.20.0       BiocInstaller_1.24.0     

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.8          plyr_1.8.4           GenomeInfoDb_1.10.1  XVector_0.14.0      
 [5] tools_3.3.2          zlibbioc_1.20.0      base64_2.0           digest_0.6.10       
 [9] memoise_1.0.0        tibble_1.2           gtable_0.2.0         graph_1.52.0        
[13] DBI_0.5-1            downloader_0.4       httr_1.2.1           stringr_1.1.0       
[17] grid_3.3.2           R6_2.2.0             tcltk_3.3.2          RBGL_1.50.0         
[21] BeadDataPackR_1.26.0 magrittr_1.5         reshape2_1.4.2       scales_0.4.1        
[25] GenomicRanges_1.26.1 assertthat_0.1       xtable_1.8-2         colorspace_1.3-2    
[29] stringi_1.1.2        openssl_0.9.5        lazyeval_0.2.0       munsell_0.4.3       
[33] illuminaio_0.16.0

Thanks,

Emilio

 

 

geneanswers • 501 views
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