Question: GenesAnswers for Arabidopsis!
0
gravatar for fufuyou
4.0 years ago by
fufuyou0
fufuyou0 wrote:

Dear Mr/Miss,

I am using your R script, GeneAnswer for GO and KEGG pathway analysis. I met a problem about how to transfer Arabidopsis gene id to EntrzGeneID. I donot know if your script work on Arabidopsis. I have tried the example data from human genome. It is work well. 

I use my Arabidopsis data that the error file is following as:

[1] "geneInput has built in ..."

Error in geneAnswersBuilder(sdgGeneInput, "org.At.tair.db", categoryType = NULL,  : 

  Annotation library can not be recognized!  Abort GeneAnswers Building ...

If I want to use Arabidopsis GO analysis, How I should change my data set?

Thank you very much,

Fuyou

Botany and Plant Pahtology Department

Purdue University

annotation • 718 views
ADD COMMENTlink modified 4.0 years ago by svlachavas660 • written 4.0 years ago by fufuyou0
Answer: GenesAnswers for Arabidopsis!
1
gravatar for svlachavas
4.0 years ago by
svlachavas660
Greece/Athens/National Hellenic Research Foundation
svlachavas660 wrote:

Dear fufuyou,

could you provide us if it is possible the sdgGeneInput you have created ? As you have possibly already know, the essential input for geneAnswers is a vector of EntrezIDs, along with other interested values, such as log-FCs, in a appropriate form of a data.frame, like the below example:

head(gene.input)
  Entrez.Gene.ID fold.change
1          11306  -0.1521352
2          11441   0.1868613
3          11518  -0.1825984
4          11535   0.1994277
5          11541  -0.2066423
6          11600  -0.1624796

and then for instance, if you want to use the Arabidopsis GO analysis, you could use the following function:

genAns<-geneAnswersBuilder(sdgGeneInput, "org.At.tair.db", categoryType="GO", known=T, geneExpressionProfile=NULL-except you also have an expression matrix)

if you check in more detail the geneAnswersBuilder function: ?geneAnswersBuilder 

you can find the explanation of each argument-also i see that the annotation library for Arabidopsis is supported, but you maybe have forgotten to install the package:

source("http://bioconductor.org/biocLite.R")
biocLite("org.At.tair.db")

Give it a try again and inform for any further problems 

Best,

Stathis

 

ADD COMMENTlink written 4.0 years ago by svlachavas660

Dear Fufuyou,

please excume me but i forgot to also mention earlier regarding your problem of " I met a problem about how to transfer Arabidopsis gene id to EntrzGeneID". If you mean Arabidopsis gene ids which have the following form: i.e. "AT2G33040"

then you should make something like the following:

ls("package:org.At.tair.db")

keys(org.At.tair.db)

columns(org.At.tair.db)

[1] "TAIR"         "CHRLOC"       "CHRLOCEND"    "ENZYME"       "PATH"        
 [6] "PMID"         "REFSEQ"       "SYMBOL"       "GENENAME"     "GO"          
[11] "EVIDENCE"     "ONTOLOGY"     "GOALL"        "EVIDENCEALL"  "ONTOLOGYALL" 
[16] "ARACYC"       "ARACYCENZYME" "ENTREZID"     "CHR"   

then for instance, if you have an example vector of Arabidopsis gene ids(if like the form from above):

example.ids <- c("AT2G35450", "AT2G35460", "AT2G35470", "AT2G35480" ,"AT2G35490" ,"AT2G35500")

res <- select(org.At.tair.db, example.ids, "ENTREZID")

and then you should have the ENTREZIDs for the arabidopsis gene ids you have used as an input

I hope this works

 

 

 

 

ADD REPLYlink modified 4.0 years ago • written 4.0 years ago by svlachavas660
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