Question: GOSemSim problem for yeast proteins
0
gravatar for horcsct
4.6 years ago by
horcsct0
Iran, Islamic Republic Of
horcsct0 wrote:

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.

yeast gosemsim • 1.0k views
ADD COMMENTlink modified 4.6 years ago by Guangchuang Yu1.1k • written 4.6 years ago by horcsct0
Answer: GOSemSim problem for yeast proteins
1
gravatar for Guangchuang Yu
4.6 years ago by
Guangchuang Yu1.1k
China/Guangzhou/Southern Medical University
Guangchuang Yu1.1k wrote:

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 COMMENTlink modified 4.6 years ago • written 4.6 years ago by Guangchuang Yu1.1k

Thanks very much.

ADD REPLYlink written 4.6 years ago by horcsct0
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