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How to run and access adjusted spectral (ASC) count data

See spectralcount for more details on the algorithm and parameters.

Run the ASC algorithm

  1. Select one or more context of your choice (for which protein grouping have been executed)
  2. Right-click and select Algorithms > Compute Adjusted Spectral Count
  3. Specify the values for Weight level and Spectral count level. Then OK.
  4. A popup message will inform that previous properties will be removed. Click yes to continue.
  5. Other ones, will inform that algorithm is finish, for each context. Click OK
  6. Save the MSI in order to store properties.

View ASC data

Actually the ASC result is only accessible

  1. directly after ASC have been run : See Bellow
  2. in comparison result : view comparemulticontexts

after ASC have been run

In the output windows, (menu View > IDE Log), algorithm information is display between — STAT ASC Result Report — and — END ASC Result Report —. Copy and paste the output into Excel to view

  • The first lines, gives the contexts involved in ASC.
  • Then first part display lines formatted as bellow:
accessionReplicate S1Replicate E1
AT1G65260.1Replicate S1= PROTEO:4 TOTAL:4 WEIGHTED:4.0Replicate E1= PROTEO:38 TOTAL:38 WEIGHTED:38.0
AT1G07320.3Replicate S1= PROTEO:15 TOTAL:15 WEIGHTED:15.0Replicate E1= PROTEO:3 TOTAL:3 WEIGHTED:3.0
AT5G15530.1Replicate S1= PROTEO:1 TOTAL:2 WEIGHTED:1.1764706 Replicate E1= PROTEO:0 TOTAL:2 WEIGHTED:0.33333334
AT1G80380.3Replicate S1= PROTEO:15 TOTAL:15 WEIGHTED:15.0Replicate E1= PROTEO:4 TOTAL:4 WEIGHTED:4.0
AT1G27300.1Replicate S1= PROTEO:- TOTAL:- WEIGHTED:-Replicate E1= PROTEO:- TOTAL:- WEIGHTED:-
  • And the second part display following lines :
accession Replicate S1 Replicate E1
AT1G65260.1Replicate S1=ProteinValues{weight=0, proteoSC=4, totalSC=4, weightedSC=4.0}Replicate E1=ProteinValues{weight=0, proteoSC=38, totalSC=38, weightedSC=38.0}
AT1G07320.3Replicate S1=ProteinValues{weight=0, proteoSC=15, totalSC=15, weightedSC=15.0}Replicate E1=ProteinValues{weight=0, proteoSC=3, totalSC=3, weightedSC=3.0}
AT5G15530.1Replicate S1=ProteinValues{weight=0, proteoSC=1, totalSC=2, weightedSC=1.1764706} Replicate E1=ProteinValues{weight=0, proteoSC=0, totalSC=2, weightedSC=0.33333334}
how_to/accessadjustedspectralcountdata.txt · Last modified: 2013/01/28 15:31 by