[BioC] cummeRbund package function diffData returns no rows for TSS features

[Asta Laiho [guest]]

Hi,

I am using cummeRbund package to analyze human RNAseq data. Everything else is working very smoothly, except that the function diffData(TSS(cuff)) returns zero rows which to me seems like an error. Other features; genes, isoforms and CDSs are returned correctly. What could be wrong?

This is what I'm doing:
cuff <- readCufflinks()
cuff
CuffSet instance with:
	 4 samples
	 22260 genes
	 37557 isoforms
	 27776 TSS
	 25411 CDS
	 133002 promoters
	 166656 splicing
	 101436 relCDS

As you can see, the resulting data frame has no rows:
diffData(TSS(cuff))
 [1] TSS_group_id   sample_1       sample_2       status         value_1       
 [6] value_2        ln_fold_change test_stat      p_value        q_value       
[11] significant   
<0 rows> (or 0-length row.names)

The following works correctly:
head(> head(diffData(CDS(cuff)) )
  CDS_id sample_1 sample_2  status  value_1  value_2 ln_fold_change
1     P1    S1       S2      OK 11.30910 19.39660    7.78320e-01
2    P10    S1       S2  NOTEST  3.25391  0.00000  -1.79769e+308
3   P100    S1       S2  NOTEST  2.26812  2.28999    1.38405e-02
4  P1000    S1       S2  NOTEST  0.00000  0.00000    0.00000e+00
5 P10000   S1       S2 LOWDATA 12.03700 17.89210    5.71841e-01
6 P10001    S1       S2  NOTEST  6.83010  4.39573   -6.35805e-01
      test_stat     p_value  q_value significant
1  -1.27958e+00 0.200693000 0.607328          no
2 -1.79769e+308 0.000624649 1.000000          no
3  -2.06580e-02 0.983519000 1.000000          no
4   0.00000e+00 1.000000000 1.000000          no
5   0.00000e+00 1.000000000 1.000000          no
6   9.72050e-01 0.331026000 1.000000          no





 -- output of sessionInfo(): 

R version 2.14.2 (2012-02-29)
Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)

locale:
[1] C/UTF-8/C/C/C/C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] cummeRbund_1.0.0 ggplot2_0.9.0    reshape_0.8.4    plyr_1.7.1      
[5] RSQLite_0.11.1   DBI_0.2-5       

loaded via a namespace (and not attached):
 [1] MASS_7.3-17        RColorBrewer_1.0-5 colorspace_1.1-1   dichromat_1.2-4   
 [5] digest_0.5.1       grid_2.14.2        memoise_0.1        munsell_0.3       
 [9] proto_0.3-9.2      reshape2_1.2.1     scales_0.2.0       stringr_0.6 

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