Dear all,

I have analysed RNAseq data to determine a set of differentially expressed genes between my groups of interest. I am now interested to determine if those genes belong to specific gene ontologies to infer different functions between my groups. I used goseq package to make GO analysis and finally obtained the list of significatively over-represented GO with their associated BH-corrected p-values. I tried to make a graphical representation of the data using the RamiGO package with the getAmigoTree function to obtain trees representing GO relations. However, some of the GO are excluded from the tree. For example, I have some GO terms, normally belonging to biological processes, which are not under the biological process parental group but just beside the biological process family. As example, I paste the code I used for one of the group.

library(RamiGO)
goID.A = c("GO:0007610", "GO:0003008", "GO:0065008", "GO:0044708", "GO:0044464", "GO:0005623", "GO:0007626", "GO:0005515", "GO:0007268", "GO:0023052", "GO:0044700", "GO:0065007", "GO:0097458", "GO:0007154", "GO:0050789", "GO:0050794")
pvalue = c(0.0001735966, 0.0004428847, 0.0018894235, 0.0042124553, 0.0045347318, 0.0071992698, 0.0071992698, 0.0185454703, 0.0231972281, 0.0238591271, 0.0238591271, 0.0238591271, 0.0269906646, 0.0269906646, 0.0320837424, 0.0338308027)
ramigo.A = getAmigoTree (goIDs = goID.A, pvalues = pvalue, pcolors = c('white', 'magenta'), psplit = c(0.1, 0.05, 0.025, 0.01, 0.00025), filename = 'RamiGO_A', picType = 'png', modeType = 'amigo', saveResult = TRUE)

I also tested the graphical representation directly on the AmiGO visualize tool, and obtain the same tree. If this is the true representation, could anyone explain me why? I don't understand why some GO are outside of the tree. Thank you in advance for your help

Best,

Nicolas

sessionInfo()

R version 3.1.1 (2014-07-10)
Platform: x86_64-apple-darwin10.8.0 (64-bit)

locale:
[1] fr_FR.UTF-8/fr_FR.UTF-8/fr_FR.UTF-8/C/fr_FR.UTF-8/fr_FR.UTF-8

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

other attached packages:
[1] goseq_1.16.2          geneLenDataBase_1.0.0 BiasedUrn_1.06.1     
[4] limma_3.20.9          RamiGO_1.10.0         gsubfn_0.6-6         
[7] proto_0.3-10 

loaded via a namespace (and not attached):
 [1] AnnotationDbi_1.26.1    base64enc_0.1-2        
 [3] BatchJobs_1.4           BBmisc_1.7             
 [5] Biobase_2.24.0          BiocGenerics_0.10.0    
 [7] BiocParallel_0.6.1      biomaRt_2.20.0         
 [9] Biostrings_2.32.1       bitops_1.0-6           
[11] brew_1.0-6              BSgenome_1.32.0        
[13] checkmate_1.4           codetools_0.2-9        
[15] DBI_0.3.1               digest_0.6.4           
[17] fail_1.2                foreach_1.4.2          
[19] GenomeInfoDb_1.0.2      GenomicAlignments_1.0.6
[21] GenomicFeatures_1.16.3  GenomicRanges_1.16.4   
[23] graph_1.42.0            grid_3.1.1             
[25] igraph_0.7.1            IRanges_1.22.10        
[27] iterators_1.0.7         lattice_0.20-29        
[29] Matrix_1.1-4            mgcv_1.8-3             
[31] nlme_3.1-117            parallel_3.1.1         
[33] png_0.1-7               Rcpp_0.11.3            
[35] RCurl_1.95-4.3          RCytoscape_1.14.0      
[37] Rsamtools_1.16.1        RSQLite_0.11.4         
[39] rtracklayer_1.24.2      sendmailR_1.2-1        
[41] stats4_3.1.1            stringr_0.6.2          
[43] tcltk_3.1.1             tools_3.1.1            
[45] XML_3.98-1.1            XMLRPC_0.3-0           
[47] XVector_0.4.0           zlibbioc_1.10.0