[BioC] cummeRbund package function diffData returns no rows for TSS features
Asta Laiho
asta.laiho at btk.fi
Thu Mar 15 09:12:16 CET 2012
Many thanks for a quick response!
I installed the version 1.1.3 and tried rebuilding the database but got the following error:
cuff <- readCufflinks(rebuild=T)
Creating database /Users/alaiho/Documents/Data-analysis/Projects/NGS/110007_Liisa_Nissinen/cufflinks/cuffdiff_output/cuffData.db
Reading /Users/alaiho/Documents/Data-analysis/Projects/NGS/110007_Liisa_Nissinen/cufflinks/cuffdiff_output/genes.fpkm_tracking
Checking samples table...
Populating samples table...
Writing genes table
Reshaping geneData table
Recasting
Error in as.data.frame(cast(genemelt, ... ~ measurement)) :
could not find function "cast"
> 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_1.1.3 reshape2_1.2.1 ggplot2_0.9.0 RSQLite_0.11.1
[5] 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] plyr_1.7.1 proto_0.3-9.2 scales_0.2.0 stringr_0.6
On Mar 15, 2012, at 5:28 AM, Loyal Goff wrote:
> Hi Asta,
> I believe that I had already fixed this bug in the newer releases of cummeRbund. Can you try to upgrade to the development cummeRbund version (1.1.3)? You will have to rebuild your cuffData.db database with this new version. Please let me know if this does not resolve your issue and I will try to work with you to get it resolved.
>
> Thanks!
>
> Cheers,
> Loyal
>
> On Mar 14, 2012, at 9:05 AM, Asta Laiho [guest] wrote:
>
>>
>> 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.
>>
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