Question: Error when I load my own data using ViSEAGO create_topGO
0
gravatar for srs204
8 months ago by
srs2040
srs2040 wrote:

Hi everyone,

I have trouble creating topGO object using my own data. Wondering if someone can help me with this!

I'm following a couple of tutorials and steps mentioned in the original ViSEAGO paper. Here are chunks from the tutorial and their links.

From the publication: ViSEAGO offers all statistical tests and algorithms developed in the Bioconductor topGO R package, taking into account the topology of GO graph by using ViSEAGO::create_topGO- data method followed by the topGO::runTestmethod.

Under 'Functional GO enrichment' in the tutorial, the following piece of code is used to generate the topGO object.

# create topGOdata for BP
BP<-ViSEAGO::create_topGOdata(
    geneSel=selection,
    allGenes=background,
    gene2GO=myGENE2GO, 
    ont="BP",
    nodeSize=5
)

I also referred to topGO's tutorial to make sure my data types are correct. Yet, there are some errors, that I have trouble dealing with.

For my data, I have the following code.

> ##################
> # create topGOdata for BP
> BP<-ViSEAGO::create_topGOdata(
+   geneSel=geneList_g1,
+   allGenes=topDiffGenes(geneList_g1),
+   gene2GO=myGENE2GO, 
+   ont="BP",
+   nodeSize=5
+ )

#error message:
allGenes contain genes redondancy.
duplicate elements were removed.
Error in .local(.Object, ...) : allGenes must be a factor with 2 levels

In my case, geneList_g1 is a named num with gene symbols and p-values (length 23 differentially expressed genes). This list already has genes with p<0.01, but even otherwise, this line gives the same error.

Using another command to creat topGO object, I get the following error.

> mysampleGOdata <- new("topGOdata",
+                     description = "my Simple session",
+                     ontology = "BP",
+                     allGenes = geneList_g1,
+                     geneSel = topDiffGenes,
+                     nodeSize = 1,
+                     annot = annFUN.db,
+                     affyLib = affyLib)

Building most specific GOs .....
    ( 0 GO terms found. )

Build GO DAG topology ..........
    ( 0 GO terms and 0 relations. )
Error in if is.na(index) || index < 0 || index > length(nd)) stop("vertex is not in graph: ",  : 
  missing value where TRUE/FALSE needed

Any help is much appreciated!! Thanks in advance! :)

ontology rna-seq viseago topgo R • 469 views
ADD COMMENTlink written 8 months ago by srs2040
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1740 users visited in the last hour