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

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