Hello all!

 

This is my first post.  Any help or suggestions would be greatly
appreciated!

 

I am trying to analyze 8 arrays (4 untreated, 4 treated; paired &
alternating) with SAM.

When I read the vignettes from 'siggenes' and looked at the sample
diagrams, I was expecting to see my 'Called' column go from some number
much closer to the number of probes on the hgu133probe2 Affy gene chip
(something like 50,000 I think) down to zero.  Why does it only start at
18?

 

I am thoroughly confused by that.

 

Thanks for any suggestions!!

 

Happy Holidays to all!!

 

---Nick Ettinger

University of Iowa

 

Here is my code:

TotalData <- ReadAffy()

chipnumber <- length(sampleNames(TotalData))

chipnames <- sampleNames(TotalData)

eset_rma <- rma(TotalData)

 

K <- chipnumber/2

eset.cl <- rep(1:K, e = 2) * rep(c(-1, 1), K)

eset.gnames <- geneNames(TotalData)

sam.out <- sam(eset_rma, eset.cl, rand = 123, gene.names = eset.gnames)

sam.out

 

SAM Analysis for the Two-Class Paired Case  

      Delta p0    False       Called      FDR

1     0.1   0.986 44.500      18          1

2     0.3   0.986 28.250      13          1

3     0.4   0.986 3.688       2           1

4     0.6   0.986 1.062       1           1

5     0.8   0.986 1.062       1           1

6     1.0   0.986 1.062       1           1

7     1.1   0.986 1.062       1           1

8     1.3   0.986 1.062       1           1

9     1.5   0.986 1.062       1           1

10    1.6   0.986 1.062       1           1

 

summary(sam.out)

 

SAM Analysis for the Two-Class Paired Case  

 s0 = 0.0646  (The 10 % quantile of the s values.) 

 Number of permutations: 16 (complete permutation) 

 MEAN number of falsely called genes is computed.

 

      Delta       p0          False       Called FDR  cutlow      cutup
j2    j1

1     0.1        0.986       44.500      18    1     -4.503      6.912
16    54674

2     0.3        0.986       28.250      13    1     -5.004      6.912
11    54674

3     0.4        0.986       3.688       2     1     -7.102      Inf
2     54676

4     0.6       0.986       1.062       1     1     -8.690      Inf
1     54676

5     0.8       0.986       1.062       1     1     -8.690      Inf
1     54676

6     1.0       0.986       1.062       1     1     -8.690      Inf
1     54676

7     1.1       0.986       1.062       1     1     -8.690      Inf
1     54676

8     1.3       0.986       1.062       1     1     -8.690      Inf
1     54676

9     1.5       0.986       1.062       1     1     -8.690      Inf
1     54676

10    1.6         0.986       1.062       1     1     -8.690      Inf
1 5   4676

 

 


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