Question: Annotating the results with associated gene symbols
0
gravatar for sss1991.f
4.6 years ago by
sss1991.f0
United States
sss1991.f0 wrote:

hi

i am new to R.I am using a windows base system. I am following the tut by Daniel Swan. After writing the following command > gene.symbols <- getSYMBOL(probeset.list$ID, "hgu133plus2") get this eror: 

Error in unlist(lookUp(x, data, "SYMBOL")) : 
  error in evaluating the argument 'x' in selecting a method for function
'unlist': Error in lookUp(x, data, "SYMBOL") : No keys provided
microarray limma • 1.1k views
ADD COMMENTlink modified 4.1 years ago by Gordon Smyth37k • written 4.6 years ago by sss1991.f0
Answer: Annotating the results with associated gene symbols
2
gravatar for James W. MacDonald
4.6 years ago by
United States
James W. MacDonald50k wrote:

You have to ensure that probeset.list$ID actually contains some data. The error indicates that it does not. In addition, you should probably use the more modern select() function. Note that you need to also ensure that you are passing in character values, rather than factors.

gns <- select(hgu133plus2.db, as.character(probeset.list$ID), "SYMBOL")
ADD COMMENTlink written 4.6 years ago by James W. MacDonald50k
Answer: Annotating the results with associated gene symbols
1
gravatar for arontommi
4.2 years ago by
arontommi10
Sweden
arontommi10 wrote:

I know this is late but if someone is googling, this will come up so here goes :
you dont have a probeset.list$ID

if you look at our dataframe you can see that there is no ID column

to fix this you use rownames as the ID column like his :
probeset.list$ID = rownames(probeset.list)

now it should run

ADD COMMENTlink written 4.2 years ago by arontommi10
Answer: Annotating the results with associated gene symbols
0
gravatar for Gordon Smyth
4.1 years ago by
Gordon Smyth37k
Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
Gordon Smyth37k wrote:

This question apparently relates to Daniel Swan's 2011 tutorial about using the simpleaffy and limma packages to analyse Affymetrix microarray data:

  http://bioinformatics.knowledgeblog.org/2011/06/20/analysing-microarray-data-in-bioconductor/

Exactly the same question has been asked before on this site:

  annotating the results with association gene symbol

The reason why Daniel Swan's code doesn't run exactly as is because the limma topTable now (in response to user requests) puts the probe IDs into the rownames of the output table rather than into a column called "ID". You can easily see this for yourself just by looking at the top table. So you just have to use rownames(probe.list) instead of probe.list$ID.

Alternatively you could follow the case study (Section 17.2) in the limma User's Guide, which is somewhat better because it puts the gene symbols in the data object right at the beginning of the analysis pipeline instead of the adding them later after the top table has been produced.

ADD COMMENTlink modified 4.1 years ago • written 4.1 years ago by Gordon Smyth37k
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