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 -- Sent via the guest posting facility at bioconductor.org.