Question: problem with annotating probeset ids.
0
gravatar for siddharth.avadhanam
4.2 years ago by
India
siddharth.avadhanam30 wrote:

Hi, 

I am trying to get through this tutorial on micrarray data analysis by daniel swan. I am however, getting stuck at the annotation part, when I try to annotate the probeset ids with the gene symbols. Here's what I'm getting 

> gene.symbols <- getSYMBOL(probeset.list, "hgu133plus2")
Error in unlist(lookUp(x, data, "SYMBOL")) : 
  error in evaluating the argument 'x' in selecting a method for function 'unlist': Error in .checkKeysAreWellFormed(keys) : 
  keys must be supplied in a character vector with no NAs

Also, the following command gives me a NULL result.
>head(probeset.list$ID)
NULL

So the problem is that there is no 'ID' column right ? How do I get around this ? 

chip-seq R genome • 2.0k views
ADD COMMENTlink written 4.2 years ago by siddharth.avadhanam30
1

can you do a head() & class() on probeset.list and show what does it look like and what is its class?

ADD REPLYlink written 4.2 years ago by komal.rathi3.4k
1

Ok a quick Google search took me here. So you need to do:

gene.symbols <- getSYMBOL(rownames(probeset.list), "hgu133plus2")
ADD REPLYlink written 4.2 years ago by komal.rathi3.4k

Thanks a ton. That sorted out my problem :) 

ADD REPLYlink written 4.2 years ago by siddharth.avadhanam30

Which tutorial? Can you link to it please.

ADD REPLYlink written 4.2 years ago by Neilfws48k
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