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Old 02-27-2015, 06:28 AM   #1
Neberir
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Location: USA

Join Date: Dec 2014
Posts: 4
Default CummeRbund Error

Hi all,

I am trying to use CummeRbund after using the Tuxedo pipeline; however, I keep getting the errors below:

cuff= readCufflinks(dbFile = "cuffData.db",dir="Z:/cuffdiff_new/",
+ gtffile = 'Z:/cuffmerge_output/merged.gtf', genome = 'Z:/reference.fa', rebuilt = T)
Reading Z:/cuffdiff_new//cds.diff
Writing CDSDiffData table
Indexing Tables...

Warning messages:
1: attributes are not identical across measure variables; they will be dropped
2: attributes are not identical across measure variables; they will be dropped
3: attributes are not identical across measure variables; they will be dropped
4: attributes are not identical across measure variables; they will be dropped

> d <- dispersionPlot(genes(cuff))
> d

Error in `$<-.data.frame`(`*tmp*`, "SCALE_X", value = 1L) :
replacement has 1 row, data has 0
In addition: Warning message:
In max(panels$ROW) : no non-missing arguments to max; returning -Inf


Any kind of help or suggestion would be appreciated.

Thanks.
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Old 03-08-2015, 02:57 PM   #2
chodar
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Location: Chile

Join Date: May 2014
Posts: 2
Default

Hi Neberir. I have the same issue here. Do you solved?

Im using Cufflinks 2.2.1 and cummeRbund 2.8.2
My sessioninfo (in windows but the problem is tha same in linux):

R version 3.1.2 (2014-10-31)
Platform: x86_64-w64-mingw32/x64 (64-bit)

locale:
[1] LC_COLLATE=Spanish_Spain.1252 LC_CTYPE=Spanish_Spain.1252
[3] LC_MONETARY=Spanish_Spain.1252 LC_NUMERIC=C
[5] LC_TIME=Spanish_Spain.1252

attached base packages:
[1] grid stats4 parallel stats graphics grDevices utils
[8] datasets methods base

other attached packages:
[1] cummeRbund_2.8.2 Gviz_1.10.10 rtracklayer_1.26.2
[4] GenomicRanges_1.18.4 GenomeInfoDb_1.2.4 IRanges_2.0.1
[7] S4Vectors_0.4.0 fastcluster_1.1.16 reshape2_1.4.1
[10] ggplot2_1.0.0 RSQLite_1.0.0 DBI_0.3.1
[13] BiocGenerics_0.12.1

loaded via a namespace (and not attached):
[1] acepack_1.3-3.3 AnnotationDbi_1.28.1 base64enc_0.1-2
[4] BatchJobs_1.5 BBmisc_1.9 Biobase_2.26.0
[7] BiocParallel_1.0.3 biomaRt_2.22.0 Biostrings_2.34.1
[10] biovizBase_1.14.1 bitops_1.0-6 brew_1.0-6
[13] BSgenome_1.34.1 checkmate_1.5.1 cluster_2.0.1
[16] codetools_0.2-10 colorspace_1.2-4 dichromat_2.0-0
[19] digest_0.6.8 fail_1.2 foreach_1.4.2
[22] foreign_0.8-63 Formula_1.2-0 GenomicAlignments_1.2.1
[25] GenomicFeatures_1.18.3 gtable_0.1.2 Hmisc_3.15-0
[28] iterators_1.0.7 lattice_0.20-30 latticeExtra_0.6-26
[31] MASS_7.3-39 matrixStats_0.14.0 munsell_0.4.2
[34] nnet_7.3-9 plyr_1.8.1 proto_0.3-10
[37] RColorBrewer_1.1-2 Rcpp_0.11.4 RCurl_1.95-4.5
[40] rpart_4.1-9 Rsamtools_1.18.2 scales_0.2.4
[43] sendmailR_1.2-1 splines_3.1.2 stringr_0.6.2
[46] survival_2.38-1 tools_3.1.2 VariantAnnotation_1.12.9
[49] XML_3.98-1.1 XVector_0.6.0 zlibbioc_1.12.0
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Old 09-03-2015, 11:55 PM   #3
znasim09
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Location: Seoul, Korea

Join Date: Sep 2015
Posts: 23
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Hey anyone solved this issue? Me too having the same problem...
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Old 09-04-2015, 02:28 AM   #4
paolo.kunder
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Location: Milano, Italy

Join Date: Aug 2011
Posts: 93
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Genome option should be genome build, for example hg19...mm10..
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Old 09-04-2015, 03:44 AM   #5
znasim09
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Location: Seoul, Korea

Join Date: Sep 2015
Posts: 23
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What about Arabidopsis ?? It's genome is not included in the UCSC
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