Question: Problem with assigning GO IDs to a list of genes
0
gravatar for cgallus
2.3 years ago by
cgallus0
cgallus0 wrote:

Hi guys,

so I want to assign GO IDs to a list of genes (I have the genname and entrez). I am using Biomart for this with the following code:

ensembl = useMart("ensembl")
ensembl = useDataset("mmusculus_gene_ensembl", mart = ensembl)

dat <- read.csv("Workbook10.csv", header = FALSE)
result1 <- getBM(attributes = c("external_gene_name", "entrezgene", "go_id""), filters = "entrezgene", values = dat, mart = ensembl)

in my workbook I have a list of mouse genes (their entrez codes)

in principle this works and I get for almost all genes their GO IDs assigned, however when I check for some examples, they are missing entirely and those are genes which definitely have GO IDs, I checked it.

Does anyone know what the problem is?

Any help would be highly appreciated!

gene R software error • 636 views
ADD COMMENTlink modified 2.3 years ago by EagleEye6.3k • written 2.3 years ago by cgallus0
0
gravatar for EagleEye
2.3 years ago by
EagleEye6.3k
Sweden
EagleEye6.3k wrote:

You can also cross check your results with GeneSCF.

Example for retrieving genes and associated terms as text file.

Orelse if you have list of genes (symbols or Entrez Ids), you can input the list to GeneSCF to annotate the list with meaningful statistics. There will be less chance that GeneSCF will miss genes since it query GeneOntology database realtime.

ADD COMMENTlink modified 2.3 years ago • written 2.3 years ago by EagleEye6.3k
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