Output from the transCount program
Below we describe the different output files of the transCount program. The
vocabulary and the symbols used here are as in the paper mentioned above.
info<outName>.txt
This file contains the following lines:
 Line 1-13:
o nofTissues = the number of samples
o startTissue = 1
o nofGenes = the number of genes
o startGene = 1
o nofArrays = the number of microarrays
o nofSets = the number of transitive experiments
o nofPens = the number of pens
o nofSpots = the number of spots
o nofProbes = the number of probe identification numbers (PIDs).
o overDisp = 1 if overdispersion, 0 otherwise
o writeAllParam = 1 if writeAllParam, 0 otherwise
o c1 = 1/c from the infile
o burnIn = burn-in/thinning from the infile
 Line 14: purity = the nofTissues purity values normalised to zero mean and
standard deviation one. (If purity is not included as a covariate the nofTissues
numbers are all zero)
 Line 15: setNumber = the nofTissues experiment numbers indicating which
transitive experiment the different samples belong to.
 Line 16: tissueNumberName =
 Then nofTissues lines: On each line a sample number with corresponding sample
name. One line for each of the sample numbers 0,…, nofTissues -1. The lines are
sorted in sample number.
 Next line: geneNumberName =
 The last nofGenes lines: On each line a gene number with corresponding gene
name. One line for each of the gene numbers 0,…, nofGenes -1. The lines are
sorted on gene number.
last<outName>.txt
This file always contains all parameter values of the last iteration written to file during
the program run. The last number on the file is the corresponding seed number.
res<outName>.txt
This file contains the traces obtained for the following parameters in the model. Each
column contains the trace for one parameter. The columns are the following:
 The first six:  0 ,  l ,  q ,  m ,  ,  'Cy 3


The next nine (ten):  a ,  e ,  p ,  t , dye ,   ,t ,  t ,  RID ,  PID ,  g and  (if
overdispersion)
The next nofArrays:  a

The next nofSets:  e
The next nofPens:  p

The next nofTissues:  tdye

The next nofTissues:  t


The next nofTissues:  t
The last line contains the current logposterior value minus the logposterior of
the initial parameter values

geneRes<outName>.txt
This file contains the traces obtained for the  g parameters.
Ktilde0Res<outName>.txt, …,
Ktilde< nofTissues -1>Res<outName>.txt
The file Ktilde<t>Res<outName>.txt contains the traces obtained for the G
~
K gt parameters. If all spots for a gene g and a sample t are flagged on all microarrays,
~
the values in the trace for the corresponding K will always be –1.0.
The rest of the files described below only exist if writeAllParam is given
ridRes<outName>.txt
This file contains the traces obtained for the  RID parameters.
pidRes<outName>.txt
This file contains the traces obtained for the  PID parameters.
epsRes<outName>.txt
This file only occurs if overdispersion is included and contains the traces obtained for
the  parameters. Each column contains the trace for one parameter and the  ’s are
sorted first on dye, then on microarray and at last on spot. If a spot s is flagged on
microarray c (i.e. flag!=0), the values in the trace for the corresponding  will always
be 0.0 and –1.0, respectively.
HRes<outName>.txt
~
This file contains the traces obtained for the H parameters. Each column contains the
~
trace for one parameter and the H ’s are sorted first on dye, then on microarray and at
last on spot. If a spot s is flagged on microarray c (i.e. flag!=0), the values in the trace
~
for the corresponding H will always be 0.0 and –1.0, respectively.