170107 limma problems - npslindstrom/DE-analysis GitHub Wiki

So today Linnea uploaded the counts_table for the Star alignment. When i tried running limma on it I got an error message that said that there were duplicates in the row.names of the table. After some experimenting in excel and R using the "duplicated()" command I were able to realize that rows 23174 to 23186 have a different formatting than the other gene names and that two of these are duplicates. I am unsure what to do. I can just remove them and continue with the analysis but I think this indicates that there is something wrong with the alignment. Linnea also mentioned that the number of counts is much lower using star than the one generated beforehand with tophat. It all seems suspect but the deadline for the poster is coming up so I don't know what we should do. We will have a group meeting on monday where we can discuss what results we can realistically present.