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Alex Buerkle used the complicated TN spreadsheet to create a list of tubes that need to be amplicon sequenced. Shannon Harris had already arranged the tubes they had sent and transcribed the hand written labels into a spreadsheet and added them to 96 tube racks. I attempted to reconcile the tobeplated list from Alex’s data manipulation with this using this r-script and these data. I was able to locate 293 of the 303 tobeplated tubes and created a pull list. I found one transcription error. There are still 10 tubes I could not locate:

I tried to delve into the data to see if I could locate these 10 samples. I did not have any luck. I do not think it is a transcription error when I anti joined samplesInSites against our spreadsheet and then the spreadsheet against samplesInSites there was no easily discernible pattern. The list of sites between the 2 even disagreed. And, there were 212-228 disagreements.

212 samples from the transcribed list do not match anything in samplesInSites (an R object that reflects the spreadsheets that came from Tennessee). These are in DisputedTubes in the R workspace.

Gregg Randolph : on line 361 of manageAlfalfa2.R, you have ShippedTubes <- samplesInSites[!(samplesInSites$site %in% unique(samplesInPlates$site)),]. I am not entirely sure what this subsetting was for, but it turns out that some (maybe all of our sample names that we thought we were missing (the 212 above) are in the samplesInSites variable, but not in ShippedTubes. For example, forty of the 212 samples, were attributable to site 107. There is not Site 107 in ShippedTubes, but these samples do appear to be in samplesInSites.

grep("^Site_107", ShippedTubes$modmodname, value = TRUE) returns no values

samplesInSites[samplesInSites == 107,]

So, something is still fishy with the TN spreadsheet concerning tubes.