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

[Loyal A. Goff]

Hi Asta,
This is a bug that has been fixed in future versions, the current workaround is to directly import the reshape library before running readCufflinks, as follows:

>library(cummeRbund)
>library(reshape)
>cuff<-readCufflinks(rebuild=T)

Cheers,
Loyal


------------------
Loyal A. Goff
Postdoctoral Fellow
CSAIL, MIT &
SCRB, Harvard

On Mar 15, 2012, at 4:12 AM, Asta Laiho <asta.laiho at btk.fi> wrote:

> 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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>> 
>