1) EMMIX-f1.f is same as EMFAC.f
2) EMMIX-f2.f is same as EMFACe.f



1) For emmix-t that is needed in select-genes and in cluster-tissues 
for ordering the gene groups in terms of the group means, modify EMMIX.max
accordingly and compile emmix.f


MNIND     120 ( upper bound on the no. of tissues)
NATT        1 (always)
MAXNG       3 (always)


2) For emmix-spher that is needed in cluster-genes in ordering the gene groups 
in terms of the group means, modify EMMIX.max accordingly and compile 
emmix-spher.f.

MNIND    5000 (upper bound on the no. of genes)
NATT      120 (upper bound on the no. of tissues)
MAXNG      50 (upper bound on the no. of groups of genes)

To run the robust version, type Y for options and then specify option 11.

3) For emmix that is needed in cluster-tissues in clustering the tissues,
modify EMMIX.max accordingly and compile emmix.f

MNIND     120 (upper bound on the no. of tissues)
NATT       60 (upper bound on the no. of genes within a group or the no.
                of groups of genes)
MAXNG       5 (upper bound on the no. of subclasses of tissues)


4) For emmix-f1 that is needed in cluster-tissues in clustering the tissues, 
modify EMMIX.max accordingly and compile emmix-f1.f

MNIND     120 (upper bound on the no. of tissues)
NATT       60 (upper bound on the no. of genes within a group or the no.
                of groups of genes)
NATTQ      10 (upper bound on the no. of factors)
MAXNG       5 (upper bound on the no. of subclasses of tissues)



5) For emmix-f2 that is needed in cluster-tissues in clustering the tissues, 
modify EMMIX.max accordingly and compile emmix-f2.f

MNIND     120  (upper bound on the no. of tissues)
NATT       60* (upper bound on the no. of genes within a group or the no.
                of groups of genes)
NATTQ      10  (upper bound on the no. of factors)
MAXNG       5  (upper bound on the no. of subclasses of tissues)

*  But in practice, this could be very large - as large as 2000, say
   but there may be problems compiling it with such a large value


The PC version is in on my c-drive in the directory 

                program filesemmixgene-pc


To compile programs needed by EMMIX-GENE, use the programs icon to go to 

                Compaq Visual Fortran 6
                Fortran command prompt

cd to appropriate directory by

                cd \microarrays\emmix-gene

To compile program emmix.f using FORTRAN 90 program, type

                f90 /fast emmix.f

after changing 

DPMPAR=    2.2250738585072D-308

(the line with d-308 in it) to

 DPMPAR=    2.22507385850721D-308

i.e. add a 1 before the D.

After file has been compiled, move the execution file emmix.exe to the
directory program files/emmixgene-pc, type

                 mv emmix.exe c:\program files\emmixgene-pc

If that doesn't work, replace program files by prog~1

To look at what is in the directory, type

                 dir


To run EMMIX-GENE, use the programs icon to go to
                /programs file/emmixgene-pc