Hi Joseph

You can also try GlobalTest,GOstat,Category and GeneAnswer package for GO
term enrichment. Here what is  the content of your CSV file?

If it is Entrez id/Probe_id then you can also use GO.db for the mapping of
entrez id to ACCNUM.

Regards

Reema Singh
PhD Scholar
Computational Biology and Bioinformatics
School of Computational and Integrative Sciences
Jawaharlal Nehru University
New Delhi-110067
INDIA



On Thu, Mar 21, 2013 at 12:17 AM, Joseph Nalluri [guest] <
guest@bioconductor.org> wrote:

>
> Hello Bioconductor group,
>
>  I am trying to derive a list of enriched GO terms from a set of genes
> given by a user. The way I understand and am implementing is:
>
> My input is a csv file consisting of about 500 genes.
>
> library(topGO)
> library(hgu133plus2.db)
> all.genes <- ls(hgu133plus2ACCNUM)
>
> data <- read.csv(file.choose(),header=FALSE)
> #Here I give an input csv file containing genes
>
> relevant.genes <- factor(as.integer(all.genes %in% data)
> names(relevant.genes) <- all.genes
> GOdata.BP <- new("topGOdata", ontology='BP', allGenes = relevant.genes,
> annotationFun = annFUN.db, affyLib = 'hgu133plus2.db')
>
> ------------
> Error in .local(.Object, ...) : allGenes must be a factor with 2 levels
> > str(relevant.genes)
>  Factor w/ 1 level "0": 1 1 1 1 1 1 1 1 1 1 ...
>  - attr(*, "names")= chr [1:54675] "1007_s_at" "1053_at" "117_at" "121_at"
> ...
>
> --------------
>
> Can you please direct me where am I going wrong? Am I right in using TopGO
> for this, even though I dont have expression values.
>
> - Joseph
>
>  -- output of sessionInfo():
>
> R version 2.15.2 (2012-10-26)
> Platform: i686-pc-linux-gnu (32-bit)
>
> locale:
>  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
>  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
>  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
>  [7] LC_PAPER=C                 LC_NAME=C
>  [9] LC_ADDRESS=C               LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
>  [1] hgu95av2.db_2.8.0    org.Hs.eg.db_2.8.0   topGO_2.10.0
>  [4] SparseM_0.96         GO.db_2.8.0          RSQLite_0.11.2
>  [7] DBI_0.2-5            AnnotationDbi_1.20.7 Biobase_2.18.0
> [10] BiocGenerics_0.4.0   graph_1.36.2
>
> loaded via a namespace (and not attached):
> [1] grid_2.15.2     IRanges_1.16.6  lattice_0.20-14 parallel_2.15.2
> [5] stats4_2.15.2   tools_2.15.2
>
> --
> Sent via the guest posting facility at bioconductor.org.
>
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