[BioC] Two class paired analysis using siggenes

[Mary Winn]

I am using siggenes to do a two class paired analysis of 36  
microarrays.  I do not appear to have any problems but upon  
summarizing the results I receive "NA" for fold change.  I believe I  
read somewhere in the vingette that fold change is only calculated for  
two class unpaired analysis.  Is this true?  If not, what must I do in  
order to calculate the fold change in a two class paired analysis?

Thanks,

Mary

University of California, San Diego

 > K<-18
 > cl<-c((1:18),-1:-18)
 > mydata<- 
as 
.matrix 
(read.table("filter.txt",header=TRUE,sep="\t",row.names=1,as.is=TRUE))
 > sam.out<-sam(mydata,cl,rand=123456)
 > sum.sam.out<-summary(sam.out,5.8)
 >sum.sam.out
SAM Analysis for the Two-Class Paired Case

s0 = 0

  Number of permutations: 100

  MEAN number of falsely called variables is computed.

Delta: 5.8
cutlow: -7.086
cutup: 6.704
p0: 0.146
Identified Genes: 7988
Falsely Called Genes: 0
FDR: 0


Identified Genes (using Delta = 5.8):

        Row d.value  stdev rawp q.value R.fold                          
Name
1    15497   60.02 0.0715    0       0     NA                  
1439466_s_at
2     7512   52.20 0.0501    0       0     NA                  
1427036_a_at
3    11424   45.64 0.0501    0       0     NA                    
1433603_at
4    22076   42.52 0.0526    0       0     NA                    
1451019_at
5    24816   42.11 0.0720    0       0     NA                  
1455269_a_at
6    13851   40.63 0.0775    0       0     NA                    
1436983_at
7    15488   40.49 0.0757    0       0     NA                  
1439455_x_at
8    25290   40.40 0.0370    0       0     NA                  
1455975_x_at
9     6774   40.08 0.0814    0       0     NA                  
1426025_s_at
10    2060   39.92 0.0629    0       0     NA                  
1418594_a_at