I have been using DAVID for a while now, but I am totally new to the DavidWebService package for R.
I load the package and initiate the analysis in a similar way to what is used as an example in the vignette for connectivity basic work flow:
R> library("RDAVIDWebService") R> david<-DAVIDWebService$new(email="firstname.lastname@example.org") R> data(demoList1) R> result<-addList(david, demoList1, + idType="AFFYMETRIX_3PRIME_IVT_ID", + listName="demoList1", listType="Gene") R> result
The problem is the
data() command. The above example uses the integrated demoList1 example dataset which contains geneids as a character vector.
I have uploaded a simple csv file containing a list of 2000 gene IDs (corresponding to OFFICIAL_GENE_SYMBOL), which of course loads as a dataframe, which I call 'genelistdavid'. However, when I run
I receive the following error:
Warning message: In data(genelistdavid) : data set ‘genelistdavid’ not found
The same thing happens when I create a new character vector from genelistdavid using as.character().
Does anyone have a fix for this failure to load my genelist into the david environment? Thanks so much.