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veitveit avatar veitveit commented on August 12, 2024

I think I identified the error:

|250000amol |    2|
  |25000amol  |    1|

Your file for the experimental design has some wrong numbers or labels. And PolySTest might fail when there is only one replicate

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pinaraltiner avatar pinaraltiner commented on August 12, 2024

I have tried with different datasets, with the following experimental design; however, the error still is the same as previously.

mzdbfile	exp_cond
./OVEMB150205_12.mzDB	1fmol
./OVEMB150205_14.mzDB	1fmol
./OVEMB150205_16.mzDB	1fmol
./OVEMB150205_18.mzDB	1fmol
./OVEMB150205_21.mzDB	10fmol
./OVEMB150205_23.mzDB	10fmol
./OVEMB150205_25.mzDB	10fmol
./OVEMB150205_27.mzDB	10fmol

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veitveit avatar veitveit commented on August 12, 2024

Strange. Also with the original UPS dataset and the correct experimental design?
Can you run another git pull to get the newest version (dev)? And get the most recent docker images via
docker pull wombatp/proline-pipeline:dev

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pinaraltiner avatar pinaraltiner commented on August 12, 2024 
mzdbfile	exp_cond
./UPS1_125amol_R2.mzDB	125amol
./UPS1_125amol_R3.mzDB	125amol
./UPS1_50amol_R1.mzDB	50amol
./UPS1_50amol_R2.mzDB	50amol
./UPS1_50amol_R3.mzDB	50amol
./UPS1_125amol_R1.mzDB	125amol

I tried to run the subset of original UPS data (shown above) after pulling the updated version of the Proline pipeline; however, I faced another error as in the below.

Error executing process > 'run_polystest (1)'

Caused by:
  Process `run_polystest (1)` terminated with an error exit status (1)

Command error:
  Error in txtProgressBar(1, NumComps) : must have 'max' > 'min'
  Calls: UnpairedDesign -> txtProgressBar
  In addition: Warning message:
  Partial NA coefficients for 256 probe(s)
  Execution halted

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