Error with makePeptideTable(evi, meta), Intensity not found
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I am having an issue generating the pepdat file. I have loaded my evi and meta files as suggested, but i get the following error
pepdat <- makePeptideTable(evi, meta)
Error in makePeptideTable(evi, meta) :
Measure 'Intensity ' from metadata not found in measure.cols.
I checked and the intensity shows up in both the evi file and the meta file.
metadata.txt
evidence.txt
Any advice would be great, thanks.
> str(measureColumns) List of 1 $ intensity: chr "Intensity"
> str(evi) 'data.frame': 81546 obs. of 10 variables: $ sequence : chr "AAAAAAASDKEGKEEEAAPSAK" "AAAAAAASDKEGKEEEAAPSAK" "AAAAAAASDKEGKEEEAAPSAK" "AAAAAAASDKEGKEEEAAPSAK" ... $ modified_sequence: chr "_AAAAAAASDKEGKEEEAAPSAK_" "_AAAAAAASDKEGKEEEAAPSAK_" "_AAAAAAASDKEGKEEEAAPSAK_" "_AAAAAAASDKEGKEEEAAPSAK_" ... $ modifications : chr "Unmodified" "Unmodified" "Unmodified" "Unmodified" ... $ protein_group : chr "HORVU1Hr1G078500.1" "HORVU1Hr1G078500.1" "HORVU1Hr1G078500.1" "HORVU1Hr1G078500.1" ... $ protein : chr "HORVU1Hr1G078500.1" "HORVU1Hr1G078500.1" "HORVU1Hr1G078500.1" "HORVU1Hr1G078500.1" ... $ experiment : chr "IE-3" "IE-4" "IE-4" "UE-4" ... $ charge : int 3 3 2 3 3 2 2 2 2 2 ... $ reverse : chr "" "" "" "" ... $ contaminant : chr "" "" "" "" ... $ intensity : num 5528900 24578000 2805700 38772000 2396400 ...
> str(meta) 'data.frame': 11 obs. of 5 variables: $ experiment: Factor w/ 11 levels "HAU-1","HAU-2",..: 1 2 3 4 5 6 7 8 9 10 ... $ measure : Factor w/ 1 level "Intensity ": 1 1 1 1 1 1 1 1 1 1 ... $ sample : Factor w/ 11 levels "HAU-1","HAU-2",..: 1 2 3 4 5 6 7 8 9 10 ... $ condition : Factor w/ 3 levels "A","B","C": 1 1 1 2 2 2 2 3 3 3 ... $ replicate : int 1 2 3 1 2 3 4 1 2 3 ...
I resolved the issue. There was a hidden space in the intensity column.
Thanks anyways,
Sebastien