GOSemSim problem for yeast proteins
1
0
Entering edit mode
horcsct • 0
@horcsct-7344
Last seen 5.6 years ago
Iran, Islamic Republic Of

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.

GOSemSim yeast • 1.2k views
ADD COMMENT
1
Entering edit mode
Guangchuang Yu ★ 1.2k
@guangchuang-yu-5419
Last seen 4 months ago
China/Guangzhou/Southern Medical Univer…

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

 

 

ADD COMMENT
0
Entering edit mode

Thanks very much.

ADD REPLY

Login before adding your answer.

Traffic: 436 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6