Dear all

I am trying to use oposSOM to analyze Affymetrix HTA 2.0 array data.

I assume that opsSOM is using the default host parameter when calling biomaRt. And the problem here is that, for any reason, using the current host, there is no HTA 2.0 annotation available.

> Ensembl <- useMart(biomart = "ENSEMBL_MART_ENSEMBL",
+                    dataset="hsapiens_gene_ensembl")
> listFilters(Ensembl)[,1][grep("affy", listFilters(Ensembl)[,1])]
 [1] "with_affy_huex_1_0_st_v2"   "with_affy_hc_g110"          "with_affy_hg_focus"         "with_affy_u133_x3p"        
 [5] "with_affy_hg_u133a"         "with_affy_hg_u133a_2"       "with_affy_hg_u133_plus_2"   "with_affy_hg_u133b"        
 [9] "with_affy_hg_u95a"          "with_affy_hg_u95av2"        "with_affy_hg_u95b"          "with_affy_hg_u95c"         
[13] "with_affy_hg_u95d"          "with_affy_hg_u95e"          "with_affy_hugenefl"         "with_affy_hugene_1_0_st_v1"
[17] "with_affy_hugene_2_0_st_v1" "with_affy_primeview"        "affy_hc_g110"               "affy_hg_focus"             
[21] "affy_hg_u95a"               "affy_hg_u95av2"             "affy_hg_u95b"               "affy_hg_u95c"              
[25] "affy_hg_u95d"               "affy_hg_u95e"               "affy_hg_u133a_2"            "affy_hg_u133a"             
[29] "affy_hg_u133b"              "affy_hg_u133_plus_2"        "affy_hugenefl"              "affy_hugene_1_0_st_v1"     
[33] "affy_hugene_2_0_st_v1"      "affy_huex_1_0_st_v2"        "affy_primeview"             "affy_u133_x3p"   

To get HTA 2.0 annotations, I have to use an archive. 

> Ensembl <- useMart(biomart = "ENSEMBL_MART_ENSEMBL",
+                    dataset="hsapiens_gene_ensembl",
+                    host = "jul2015.archive.ensembl.org")
> listFilters(Ensembl)[,1][grep("affy", listFilters(Ensembl)[,1])]
 [1] "with_affy_huex_1_0_st_v2"   "with_affy_hc_g110"          "with_affy_hg_focus"         "with_affy_u133_x3p"        
 [5] "with_affy_hg_u133a"         "with_affy_hg_u133a_2"       "with_affy_hg_u133_plus_2"   "with_affy_hg_u133b"        
 [9] "with_affy_hg_u95a"          "with_affy_hg_u95av2"        "with_affy_hg_u95b"          "with_affy_hg_u95c"         
[13] "with_affy_hg_u95d"          "with_affy_hg_u95e"          "with_affy_hugenefl"         "with_affy_hugene_1_0_st_v1"
[17] "with_affy_hugene_2_0_st_v1" "with_affy_hta_2_0"          "with_affy_primeview"        "affy_hc_g110"              
[21] "affy_hg_focus"              "affy_hg_u95a"               "affy_hg_u95av2"             "affy_hg_u95b"              
[25] "affy_hg_u95c"               "affy_hg_u95d"               "affy_hg_u95e"               "affy_hg_u133a_2"           
[29] "affy_hg_u133a"              "affy_hg_u133b"              "affy_hg_u133_plus_2"        "affy_hta_2_0"              
[33] "affy_hugenefl"              "affy_hugene_1_0_st_v1"      "affy_hugene_2_0_st_v1"      "affy_huex_1_0_st_v2"       
[37] "affy_primeview"             "affy_u133_x3p" ​

Is it possible to give oposSOM additional arguments to set up the biomaRt connexion ? 

Thanks a lot !

Hello,

I am afraid that the missing Affymetrix HTA 2.0 annotation for human in Ensembl release 84 is a known bug (Please see following page for details: http://www.ensembl.info/contact-us/known-bugs/).

We will aim to fix this issue for our next release e!85.

Apologies for any inconvenience caused,

Regards,

Thomas