I have a problem when I try to use GOSemSim to calculate the GO semantic similarities between yeast proteins.

geneSim("852494", "854869", ont = "MF", organism="yeast", measure="Resnik")

return below result:

[1] NA
Warning messages:
1: In is.na(go) : is.na() applied to non-(list or vector) of type 'NULL'
2: In is.na(go) : is.na() applied to non-(list or vector) of type 'NULL'

Any comments or advice are welcome.

Thanks.

Hi,

The annotation of yeast is based on the ORF ID, but not Entrez Gene ID.

ORF ID is also the default key of annotation package org.Sc.sgd.db as shown below:

> head(keys(org.Sc.sgd.db), n=30)
 [1] "15S_rRNA" "21S_rRNA" "AIP5"     "ARS1001"  "ARS1002"  "ARS1003"
 [7] "ARS1004"  "ARS1005"  "ARS1006"  "ARS1007"  "ARS1008"  "ARS1009"
[13] "ARS1010"  "ARS1011"  "ARS1012"  "ARS1013"  "ARS1014"  "ARS1015"
[19] "ARS1016"  "ARS1017"  "ARS1018"  "ARS1019"  "ARS102"   "ARS1020"
[25] "ARS1021"  "ARS1022"  "ARS1023"  "ARS1024"  "ARS1025"  "ARS103"
>

You should firstly convert your entrez gene ID to orf ID before using geneSim.

> select(org.Sc.sgd.db, keys=c("852494", "854869"), keytype="ENTREZID", columns="ORF")
  ENTREZID     ORF        SGD
1   852494 YBR195C S000000399
2   854869 YML102W S000004570
> geneSim("YBR195C", "YML102W", ont = "MF", organism="yeast", measure="Resnik")
$geneSim
[1] 0.606

$GO1
[1] "GO:0042393"

$GO2
[1] "GO:0042393"

Bests,

Guangchuang