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Question: annotating the results with association gene symbol
1
4.7 years ago by
Guest User12k
Guest User12k 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$ID, "hgu133plus2") get this eror: Error in unlist(lookUp(x, data, "SYMBOL")) : error in evaluating the argument 'x' in selecting a method for function 'unlist': Error in lookUp(x, data, "SYMBOL") : No keys provided Can any one help. rabia ADD COMMENTlink modified 3.6 years ago by Gordon Smyth35k • written 4.7 years ago by Guest User12k 0 4.7 years ago by Tunisia Cherif Ben Hamda150 wrote: Hi Rabia, I'm new on R like you but i have some experience with this type of analysis So in your case verify that your probeset.list contain some gene DE !! att the first tap this : head(probeset.list) and told me the result !! ADD COMMENTlink modified 3.6 years ago by Gordon Smyth35k • written 4.7 years ago by Cherif Ben Hamda150 0 3.6 years ago by France/Strasbourg/INSERM U1118 Alexandre Henriques0 wrote: Dear all, I came up to the same error, following the same tutorial. As suggested above, I tried "head(probeset.list) ". Here are the results: logFC AveExpr t P.Value adj.P.Val B 204779_s_at 7.367790 4.171707 72.77347 3.284937e-15 8.969850e-11 20.25762 207016_s_at 6.936667 4.027733 57.39252 3.694641e-14 5.044293e-10 19.44987 209631_s_at 5.192949 4.003992 51.24892 1.170273e-13 1.065182e-09 18.96660 242809_at 6.433238 4.168870 48.51842 2.043082e-13 1.394710e-09 18.70852 205893_at 4.480331 3.543714 40.56477 1.261400e-12 6.888757e-09 17.75050 204882_at -5.353547 6.513690 -34.70646 6.141288e-12 2.395629e-08 16.77396 Any idea ? Thanks, Alexandre [EDIT] I made it work thanks to a comment from a thread in another forum. http://stackoverflow.com/questions/22970546/microarray-limma-package-in-toptable-function-dont-assign-id-for-probsets-colu When "probeset.list$ID"  is changed to "rownames(probeset.list)", the error is fixed. This error was mmost likely to an update of limma, as far as I understood

You can see for yourself from the table that there isn't any column called "ID". In R parlance, the row identifiers are row names rather than a column of the table.

0
3.6 years ago by
Gordon Smyth35k
Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
Gordon Smyth35k wrote:

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

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

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 pipelline instead of the adding them later after the top table has been produced.