GoProfiler compareGeneLists Error
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Entering edit mode
2.3 years ago
Diango • 0

I would like to do a comparison analysis of two different gene lists expressed between two samples with Goprofiler, following the instructions in the manual. I remind you that I am working on the species plamoduim faliciparum (Malaria) but in the comparisonGeneLists I have the following error:

library(goProfiles)
library(org.Pf.plasmo.db)
gene <- c("PF3D7_0100200",
"PF3D7_0100800",
"PF3D7_0102200",
"PF3D7_0102700",
"PF3D7_0106400",
"PF3D7_0108500",
"PF3D7_0112100",
"PF3D7_0113300",
"PF3D7_0113700",
"PF3D7_0114400",
"PF3D7_0115400",
"PF3D7_0200200",
"PF3D7_0200700",
"PF3D7_0202100",
"PF3D7_0202200",
"PF3D7_0202500",
"PF3D7_0205000",
"PF3D7_0205100",
"PF3D7_0205200",
"PF3D7_0209000",
"PF3D7_0210800")
MF.Profiles <-basicProfile(genelist=gene, onto='MF', level=2, orgPackage="org.Pf.plasmo.db")
print(MF.Profiles)


Output :

$MF Description GOID Frequency 5 antioxidant activity GO:0016209 0 4 binding GO:0005488 3 7 cargo receptor activity GO:0038024 0 1 catalytic activity GO:0003824 0 14 molecular carrier activity GO:0140104 0  <h6>#</h6> # Comparaison : gene1 <- c("PF3D7_0100200", "PF3D7_0102200", "PF3D7_0108500", "PF3D7_0114400", "PF3D7_0202200", "PF3D7_0202500", "PF3D7_0205000", "PF3D7_0205100 ", "PF3D7_0205200 ", "PF3D7_0209000 ", "PF3D7_0219700 ", "PF3D7_0220400 ", "PF3D7_0221300 ", "PF3D7_0221500 ", "PF3D7_0223100 ", "PF3D7_0301800 ", "PF3D7_0315200 ", "PF3D7_0315300 ", "PF3D7_0402900 ", "PF3D7_0408000 ", "PF3D7_0412600 ", "PF3D7_0412900 ", "PF3D7_0413400 ", "PF3D7_0420900 ", "PF3D7_0423800 ") gene1Compared<- compareGeneLists (gene, gene1, level=2, onto="MF", orgPackage="org.Pf.plasmo.db") print(gene1Compared)  output : Error in GOTermsList(commonGenes, orgPkg = "org.Hs.eg.db", onto = onto) : require(orgPkg, character.only = TRUE, quietly = TRUE, warn.conflicts = FALSE) is not TRUE In addition: Warning message: In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, : there is no package called ‘org.Hs.eg.db’  I work on the database org.Pf.plasmo.db and in error talks about the human database. I can't understand that. Your suggestions will be beneficial RNA-Seq gene rna-seq ChIP-Seq genome • 722 views ADD COMMENT 0 Entering edit mode 2.3 years ago Prakash ★ 2.2k I tried to reproduce your problem, however, in my case, I didn' get the error that you encountered. Here is the output that I got > print(gene1Compared)$MF

linear combination of chi-squares statistic

data:  expanded1[[i]] and expanded2[[i]] and NULL
(n*m/(n+m)) * d2 = 0.97619, number of classes = 2.00000, coef1 = 0.11052, coef2 = 0.00000,
p-value = 0.002961
alternative hypothesis: true squared Euclidean distance between the contracted profiles is greater than zero
95 percent confidence interval:
0.3907884 0.5389169
sample estimates:
sample squared Euclidean distance
0.4648526
attr(,"se")
distance standard error
0.03778858


you have included space in few of the ORF name while creating gene1 object, correct it an just try once again.