Hi,

I'm doing a study that analyzes RNA-seq results from mouse and Candida albicans. For each organism, I have six different conditions. For a pathway analysis I used the Pathview package with the multi-state option, and it worked pretty fine with mice data. Bellow the code used for mouse data:

>  pv.out=pathview(gene.data=tab[,1:6], gene.idtype ="ENSEMBL", pathway.id="06016" ,
              species="mmu",out.suffix="Huntington", kegg.native = T,limit=2, res=300)

However, when I try to analyze Candida data, I get the following error:

> pv.out=pathview(gene.data=tab[,1:6], gene.idtype ="GENENAME", pathway.id="03440",
+                 species="cal",out.suffix="MAPK", kegg.native = T,limit=2, res=300)
Error in pathview(gene.data = tab[, 1:6], gene.idtype = "GENENAME", pathway.id = "03440",  :
  No proper gene annotation package available!

Candida's results were annotated using Gene name as ID from the gff file from the Candida Genome database.  I am aware that KEGG database includes C. albicans data, so I wonder what the problem might be.

I really appreciate any kind of help.

Best regards.

Daniel

> sessionInfo()
R version 3.2.1 (2015-06-18)
Platform: x86_64-apple-darwin10.8.0 (64-bit)
Running under: OS X 10.7.5 (Lion)

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

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

other attached packages:
 [1] org.Mm.eg.db_3.2.3   pathview_1.10.1      org.Hs.eg.db_3.2.3   RSQLite_1.0.0       
 [5] DBI_0.3.1            AnnotationDbi_1.32.0 IRanges_2.4.1        S4Vectors_0.8.2     
 [9] Biobase_2.30.0       BiocGenerics_0.16.1

loaded via a namespace (and not attached):
 [1] graph_1.48.0      KEGGgraph_1.28.0  XVector_0.10.0    magrittr_1.5      zlibbioc_1.16.0  
 [6] R6_2.1.1          stringr_1.0.0     httr_1.0.0        tools_3.2.1       grid_3.2.1       
[11] png_0.1-7         Rgraphviz_2.14.0  KEGGREST_1.10.0   stringi_1.0-1     Biostrings_2.38.0
[16] XML_3.98-1.3