[BioC] easyRNASeq for miRNA read counts

Vicky Chu [guest] guest at bioconductor.org
Mon Nov 18 05:12:47 CET 2013


I am looking to use DESeq to analyze my 18-29 nt small RNA libraries. Is it appropriate to prepare a  countDataSet that counts "transcripts" , or possibly "features" in this case? What do you recommend? 

Thank you! 

 -- output of sessionInfo(): 

R version 3.0.2 (2013-09-25)
Platform: x86_64-apple-darwin10.8.0 (64-bit)

[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

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

other attached packages:
 [1] easyRNASeq_1.8.1       ShortRead_1.20.0       Rsamtools_1.14.1       GenomicRanges_1.14.3  
 [5] DESeq_1.14.0           lattice_0.20-24        locfit_1.5-9.1         Biostrings_2.30.1     
 [9] XVector_0.2.0          IRanges_1.20.5         edgeR_3.4.0            limma_3.18.3          
[13] biomaRt_2.18.0         Biobase_2.22.0         genomeIntervals_1.18.0 BiocGenerics_0.8.0    
[17] intervals_0.14.0      

loaded via a namespace (and not attached):
 [1] annotate_1.40.0      AnnotationDbi_1.24.0 bitops_1.0-6         DBI_0.2-7           
 [5] genefilter_1.44.0    geneplotter_1.40.0   grid_3.0.2           hwriter_1.3         
 [9] latticeExtra_0.6-26  LSD_2.5              RColorBrewer_1.0-5   RCurl_1.95-4.1      
[13] RSQLite_0.11.4       splines_3.0.2        stats4_3.0.2         survival_2.37-4     
[17] tools_3.0.2          XML_3.95-0.2         xtable_1.7-1         zlibbioc_1.8.0      

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