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Question: RDAVIDWebService Input Incorrect
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gravatar for johntoomey
14 months ago by
johntoomey0
johntoomey0 wrote:

I am trying to build an R script for an automated GO enrichment analysis using RDAVIDWebService. In the process of doing so, I am attempting to make sure I can get the input properly formatted in order to submit it. However, I cannot get an input that works in the browser-based DAVID tool to work when using RDAVIDWebService. I'm new to R, so it's entirely possible that I have things formatted or input incorrectly.

Right now, I am trying to use the SGD_ID idType to submit my jobs, and I have all of my genes of interest converted into SGD IDs. When I submit them as a .txt file to the browser-based DAVID tool and select the "SGD_ID" idType, I get the expected results. However, when I load the gene names into RStudio and run it using the command:

result<- addList(david, mydata, idType="SGD_ID", listName="m", listType="Gene")

where mydata is the R variable holding the IDs, and I get the following error message: 

Warning message:
In object$addList(inputIds, idType, listName, listType[1]) :
  More than half of the list is not present in DAVID. Check ifthe list match the id type!!!

I've run the same analysis with the same genes in R, but with their systematic names, and a different idType and have gotten results (though some genes are unmapped), but I'm confused as to why using "SGD_ID" in RDAVIDWebService does not work. I would prefer to use the SGD IDs because I do not know which other idType to use with the systematic names. Am I likely doing something wrong when uploading the SGD IDs or am I using the command incorrectly?

ADD COMMENTlink modified 14 months ago • written 14 months ago by johntoomey0
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