Hi, I am trying out the pipeline published in Trapnell et als Nature Protocols paper <http: www.nature.com="" nprot="" journal="" v7="" n3="" full="" nprot.2012.016.html=""> . I am getting an error in cummeRbund when I try to create the cuff_data object (under R_2.15, couldn't install on 2.13 or 2.14(?)). After the first attempt to create the database the error occurs. When I rerun it generates a CuffSet but with same parameters even if datasets are different. > cuff_data<-readCufflinks("bam_cuffDiff") Creating database bam_cuffDiff/cuffData.db Reading bam_cuffDiff/genes.fpkm_tracking Checking samples table... Populating samples table... Writing genes table Reshaping geneData table Recasting Writing geneData table Error in sqliteExecStatement(con, statement, bind.data) : RS-DBI driver: (unable to bind data for parameter ':status') > cuff_data Error: object 'bamCuff' not found > cuff_data<-readCufflinks("bam_cuffDiff") > bamCuff CuffSet instance with: 1 samples 24493 genes 0 isoforms 0 TSS 0 CDS 0 promoters 0 splicing 0 relCDS I have more than 1 sample (14 samples, divided into 2 groups). My cuffdiff call seems ok to me(?): cuffdiff -o bam_cuffDiff -b /data/shared/genomes/UMD_3.1/Bos_taurus.UMD3.1.64.fa -p 12 -L FertP,FertN -u ./merged_asm/merged.gtf /BAM/E_1,./BAM/E_3,./BAM/E_4,./BAM/E_5,./BAM/E_7,./BAM/E_22,./BAM/E_25 /BAM/E_8,./BAM/E_11,./BAM/E_12,./BAM/E_13,./BAM/E_17,./BAM/E_18,./BAM/ E _21 The only other instance of this error <http: rna-seqblog.com="" data-analysis="" protocol-differential-gene-and-="" tra="" nscript-expression-analysis-of-rna-seq-experiments-with-tophat-and-="" cuffl="" inks=""/> (in comments) seems due to incorrect cuffdiff call. I have linked to the BAM files here but tried without the link. Output is generated in each case and gives same results. I hope someone has some advice=) Bruce. > sessionInfo() R version 2.15.0 (2012-03-30) Platform: i386-pc-mingw32/i386 (32-bit) locale: [1] LC_COLLATE=English_Ireland.1252 LC_CTYPE=English_Ireland.1252 [3] LC_MONETARY=English_Ireland.1252 LC_NUMERIC=C [5] LC_TIME=English_Ireland.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] cummeRbund_1.2.0 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] colorspace_1.1-1 dichromat_1.2-4 digest_0.5.2 grid_2.15.0 [5] MASS_7.3-17 memoise_0.1 munsell_0.3 plyr_1.7.1 [9] proto_0.3-9.2 RColorBrewer_1.0-5 scales_0.2.0 stringr_0.6 Bruce Moran MSc., Walsh Fellowship PhD Candidate, Systems Biology Group, Animal Bioscience and Research Dept., Teagasc, Dunsany, Co. Meath, Ireland. ---------------------------------------------------------------------- -------- Attention: This e-mail is privileged and confidential. If you are not the intended recipient please delete the message and notify the sender. Any views or opinions presented are solely those of the author. This email was scanned by Teagasc and has been certified virus free with the pattern file currently in use. This however cannot guarantee that it does not contain malicious content. Tabhair aire: Ta an r-phost seo faoi phribhleid agus faoi run. Mura tusa an duine a bhi beartaithe leis an teachtaireacht seo a fhail, scrios e le do thoil agus cuir an seoltoir ar an eolas. Is leis an udar amhain aon dearcai no tuairimi a leiritear. Scanadh an r-phost seo le Teagasc agus deimhniodh go raibh se saor o vioras leis an bpatrunchomhad ata in usaid faoi lathair. Ni feidir a rathu leis seo afach nach bhfuil abhar mailiseach ann. [[alternative HTML version deleted]]