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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.

To make progress understanding where these samples might have come from, I looked at what there sample type was:

table(gsub("^Site_[[:digit:]]+(.*)[[:digit:]]+$", "\1", DisputedTubes$Sample))

       _Alf_Epi             Alf_Epi Site_129_Alf_Epi_5_                Soil 
              1                  89                   1                  16 
     Trans_Endo           Trans_Epi 
             74                  31 

Most of the samples are from sites 105, 106, and 107.

table(gsub("^Site_([[:digit:]]+)_.*$", "\1", DisputedTubes$Sample))

101 103 104 105 106 107 108 109 110 116 120 125 126 129 134
1 10 10 40 39 40 4 15 14 10 2 7 9 2 9Gregg 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,]

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