Hi, yes sorry, i forgot to add it. yes the two names are but the same, the htseqcount is the complete table as posted in the mail, the countTalbe is the same table but only with the columns 1,2 and 6 > countTalbe SampleName FileName comparison 1 G1_I_C G1_I_C.htseq_count.txt control_Input 2 G1_I_G2 G1_I_G2.htseq_count.txt GLD2_KO_Input ... Here is the sessionInfo() > sessionInfo() R version 3.0.2 (2013-09-25) Platform: x86_64-unknown-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] parallel stats graphics grDevices utils datasets methods [8] base other attached packages: [1] edgeR_3.3.8 limma_3.17.26 DESeq_1.13.3 [4] lattice_0.20-23 locfit_1.5-9.1 Rsamtools_1.13.48 [7] Biostrings_2.29.19 GenomicFeatures_1.13.47 AnnotationDbi_1.23.27 [10] Biobase_2.21.7 GenomicRanges_1.13.51 XVector_0.1.4 [13] IRanges_1.19.38 BiocGenerics_0.7.5 BiocInstaller_1.11.4 loaded via a namespace (and not attached): [1] annotate_1.39.0 biomaRt_2.17.3 bitops_1.0-6 [4] BSgenome_1.29.1 DBI_0.2-7 genefilter_1.43.0 [7] geneplotter_1.39.05 grid_3.0.2 RColorBrewer_1.0-5 [10] RCurl_1.95-4.1 RSQLite_0.11.4 rtracklayer_1.21.12 [13] splines_3.0.2 stats4_3.0.2 survival_2.37-4 [16] tools_3.0.2 XML_3.98-1.1 xtable_1.7-1 [19] zlibbioc_1.7.0 cu, Assa On Thu, Oct 10, 2013 at 3:58 PM, Wolfgang Huber <whuber@embl.de> wrote: > Dear Assa > > Thank you for your report. Always nice to hear when R gives people a > massage. To complete your report, can you send the output of > "sessionInfo()"? > > I noted that in your code example, the table of input files is called > differently: > - htseqcount > - countTalbe > Which is the one you are actually using? > > Thanks, > Wolfgang > > On 10 Oct 2013, at 15:12, Assa Yeroslaviz <frymor@gmail.com> wrote: > > > Hi, > > > > I'm trying to create a count data set from the htseq files I created > using > > htseq-count as described in the DESeq manual. > > > > But I keep getting an error massage. > > > > This is my design table: > > > >> htseqcount > > SampleName FileName condition replicate libType > > comparison > > 1 G1_I_C G1_I_C.htseq_count.txt control G1 Input > > control_Input > > 2 G1_I_G2 G1_I_G2.htseq_count.txt GLD2_KO G1 Input > > GLD2_KO_Input > > 3 G1_I_G4 G1_I_G4.htseq_count.txt GLD4_KO G1 Input > > GLD4_KO_Input > > 4 G1_NP_C G1_NP_C.htseq_count.txt control G1 Nonpolysomal > > control_Nonpolysomal > > 5 G1_NP_G2 G1_NP_G2.htseq_count.txt GLD2_KO G1 > > Nonpolysomal GLD2_KO_Nonpolysomal > > 6 G1_NP_G4 G1_NP_G4.htseq_count.txt GLD4_KO G1 > > Nonpolysomal GLD4_KO_Nonpolysomal > > 7 G1_P_C G1_P_C.htseq_count.txt control G1 Polysomal > > control_Polysomal > > 8 G1_P_G2 G1_P_G2.htseq_count.txt GLD2_KO G1 Polysomal > > GLD2_KO_Polysomal > > 9 G1_P_G4 G1_P_G4.htseq_count.txt GLD4_KO G1 Polysomal > > GLD4_KO_Polysomal > > 10 G2_I_C G2_I_C.htseq_count.txt control G2 Input > > control_Input > > 11 G2_I_G2 G2_I_G2.htseq_count.txt GLD2_KO G2 Input > > GLD2_KO_Input > > 12 G2_I_G4 G2_I_G4.htseq_count.txt GLD4_KO G2 Input > > GLD4_KO_Input > > 13 G2_NP_C G2_NP_C.htseq_count.txt control G2 > > Nonpolysomal control_Nonpolysomal > > 14 G2_NP_G2 G2_NP_G2.htseq_count.txt GLD2_KO G2 > > Nonpolysomal GLD2_KO_Nonpolysomal > > 15 G2_NP_G4 G2_NP_G4.htseq_count.txt GLD4_KO G2 > > Nonpolysomal GLD4_KO_Nonpolysomal > > 16 G2_P_C G2_P_C.htseq_count.txt control G2 Polysomal > > control_Polysomal > > 17 G2_P_G2 G2_P_G2.htseq_count.txt GLD2_KO G2 Polysomal > > GLD2_KO_Polysomal > > 18 G2_P_G4 G2_P_G4.htseq_count.txt GLD4_KO G2 Polysomal > > GLD4_KO_Polysomal > > 19 G3_I_C G3_I_C.htseq_count.txt control G3 Input > > control_Input > > 20 G3_I_G2 G3_I_G2.htseq_count.txt GLD2_KO G3 Input > > GLD2_KO_Input > > 21 G3_I_G4 G3_I_G4.htseq_count.txt GLD4_KO G3 Input > > GLD4_KO_Input > > 22 G3_NP_C G3_NP_C.htseq_count.txt control G3 > > Nonpolysomal control_Nonpolysomal > > 23 G3_NP_G2 G3_NP_G2.htseq_count.txt GLD2_KO G3 > > Nonpolysomal GLD2_KO_Nonpolysomal > > 24 G3_NP_G4 G3_NP_G4.htseq_count.txt GLD4_KO G3 > > Nonpolysomal GLD4_KO_Nonpolysomal > > 25 G3_P_C G3_P_C.htseq_count.txt control G3 Polysomal > > control_Polysomal > > 26 G3_P_G2 G3_P_G2.htseq_count.txt GLD2_KO G3 Polysomal > > GLD2_KO_Polysomal > > 27 G3_P_G4 G3_P_G4.htseq_count.txt GLD4_KO G3 Polysomal > > GLD4_KO_Polysomal > > > > The files are all in a directory called" HTSEQ_COUNT", which is in the > same > > directory I am working in. I have 27 files in this folder. > >> dir("HTSEQ_COUNT/") > > [1] "G1_I_C.htseq_count.txt" "G1_I_G2.htseq_count.txt" > > [3] "G1_I_G4.htseq_count.txt" "G1_NP_C.htseq_count.txt" > > [5] "G1_NP_G2.htseq_count.txt" "G1_NP_G4.htseq_count.txt" > > [7] "G1_P_C.htseq_count.txt" "G1_P_G2.htseq_count.txt" > > [9] "G1_P_G4.htseq_count.txt" "G2_I_C.htseq_count.txt" > > [11] "G2_I_G2.htseq_count.txt" "G2_I_G4.htseq_count.txt" > > [13] "G2_NP_C.htseq_count.txt" "G2_NP_G2.htseq_count.txt" > > [15] "G2_NP_G4.htseq_count.txt" "G2_P_C.htseq_count.txt" > > [17] "G2_P_G2.htseq_count.txt" "G2_P_G4.htseq_count.txt" > > [19] "G3_I_C.htseq_count.txt" "G3_I_G2.htseq_count.txt" > > [21] "G3_I_G4.htseq_count.txt" "G3_NP_C.htseq_count.txt" > > [23] "G3_NP_G2.htseq_count.txt" "G3_NP_G4.htseq_count.txt" > > [25] "G3_P_C.htseq_count.txt" "G3_P_G2.htseq_count.txt" > > [27] "G3_P_G4.htseq_count.txt" > > > > This is the command I am using to create the count data set object. > > > >> newCountDataSetFromHTSeqCount(countTalbe, directory="HTSEQ_COUNT/") > > > > But it keeps spitting this error massage: > > > > Error in `colnames<-`(`*tmp*`, value = 1:27) : > > attempt to set 'colnames' on an object with less than two dimensions > > > > I even tried to reduce the size of the htseqCountTable to only three > > columns, but it still gives the same erorr. > > > > Does anyone have an idea why I get this error? > > > > > > Thanks > > > > Assa > > > > [[alternative HTML version deleted]] > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor@r-project.org > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > > [[alternative HTML version deleted]]

Hi again, ok, I have found my problem. This has nothing to do with the DESeq package, but with the output I am getting from htseq-count. I was wondering what it is but I couldn't find any information. These are the first few lines from my htseq-count output: 8060 21ur-1 0 21ur-10 0 21ur-100 0 21ur-1000 0 21ur-10000 0 21ur-10001 0 21ur-10002 0 21ur-10003 0 21ur-10004 0 So the first line has only one item. I couldn't find anything about this line. What does this number suppose to say? It is not the number of genes with or without counts, it is not the number of reads and not the sample name. Each of my file get such a number, but they seems to be random. This is the command I am using for htseq-count for file in `ls -1 *.bam` do NEW_FILE=$(echo $file | sed "s/.bam//") samtools index $file; samtools view -h -o $NEW_FILE.sam $file; *htseq-count -s no $NEW_FILE.sam ~/genomes/celegans/Caenorhabditis_elegans/UCSC/ce10/Annotation/Genes/g enes.gtf > $NEW_FILE.htseq_count.txt;* echo "done with file $file \n" done What might be the reason for this first line? thanks Assa On Thu, Oct 10, 2013 at 3:58 PM, Wolfgang Huber <whuber@embl.de> wrote: > Dear Assa > > Thank you for your report. Always nice to hear when R gives people a > massage. To complete your report, can you send the output of > "sessionInfo()"? > > I noted that in your code example, the table of input files is called > differently: > - htseqcount > - countTalbe > Which is the one you are actually using? > > Thanks, > Wolfgang > > On 10 Oct 2013, at 15:12, Assa Yeroslaviz <frymor@gmail.com> wrote: > > > Hi, > > > > I'm trying to create a count data set from the htseq files I created > using > > htseq-count as described in the DESeq manual. > > > > But I keep getting an error massage. > > > > This is my design table: > > > >> htseqcount > > SampleName FileName condition replicate libType > > comparison > > 1 G1_I_C G1_I_C.htseq_count.txt control G1 Input > > control_Input > > 2 G1_I_G2 G1_I_G2.htseq_count.txt GLD2_KO G1 Input > > GLD2_KO_Input > > 3 G1_I_G4 G1_I_G4.htseq_count.txt GLD4_KO G1 Input > > GLD4_KO_Input > > 4 G1_NP_C G1_NP_C.htseq_count.txt control G1 Nonpolysomal > > control_Nonpolysomal > > 5 G1_NP_G2 G1_NP_G2.htseq_count.txt GLD2_KO G1 > > Nonpolysomal GLD2_KO_Nonpolysomal > > 6 G1_NP_G4 G1_NP_G4.htseq_count.txt GLD4_KO G1 > > Nonpolysomal GLD4_KO_Nonpolysomal > > 7 G1_P_C G1_P_C.htseq_count.txt control G1 Polysomal > > control_Polysomal > > 8 G1_P_G2 G1_P_G2.htseq_count.txt GLD2_KO G1 Polysomal > > GLD2_KO_Polysomal > > 9 G1_P_G4 G1_P_G4.htseq_count.txt GLD4_KO G1 Polysomal > > GLD4_KO_Polysomal > > 10 G2_I_C G2_I_C.htseq_count.txt control G2 Input > > control_Input > > 11 G2_I_G2 G2_I_G2.htseq_count.txt GLD2_KO G2 Input > > GLD2_KO_Input > > 12 G2_I_G4 G2_I_G4.htseq_count.txt GLD4_KO G2 Input > > GLD4_KO_Input > > 13 G2_NP_C G2_NP_C.htseq_count.txt control G2 > > Nonpolysomal control_Nonpolysomal > > 14 G2_NP_G2 G2_NP_G2.htseq_count.txt GLD2_KO G2 > > Nonpolysomal GLD2_KO_Nonpolysomal > > 15 G2_NP_G4 G2_NP_G4.htseq_count.txt GLD4_KO G2 > > Nonpolysomal GLD4_KO_Nonpolysomal > > 16 G2_P_C G2_P_C.htseq_count.txt control G2 Polysomal > > control_Polysomal > > 17 G2_P_G2 G2_P_G2.htseq_count.txt GLD2_KO G2 Polysomal > > GLD2_KO_Polysomal > > 18 G2_P_G4 G2_P_G4.htseq_count.txt GLD4_KO G2 Polysomal > > GLD4_KO_Polysomal > > 19 G3_I_C G3_I_C.htseq_count.txt control G3 Input > > control_Input > > 20 G3_I_G2 G3_I_G2.htseq_count.txt GLD2_KO G3 Input > > GLD2_KO_Input > > 21 G3_I_G4 G3_I_G4.htseq_count.txt GLD4_KO G3 Input > > GLD4_KO_Input > > 22 G3_NP_C G3_NP_C.htseq_count.txt control G3 > > Nonpolysomal control_Nonpolysomal > > 23 G3_NP_G2 G3_NP_G2.htseq_count.txt GLD2_KO G3 > > Nonpolysomal GLD2_KO_Nonpolysomal > > 24 G3_NP_G4 G3_NP_G4.htseq_count.txt GLD4_KO G3 > > Nonpolysomal GLD4_KO_Nonpolysomal > > 25 G3_P_C G3_P_C.htseq_count.txt control G3 Polysomal > > control_Polysomal > > 26 G3_P_G2 G3_P_G2.htseq_count.txt GLD2_KO G3 Polysomal > > GLD2_KO_Polysomal > > 27 G3_P_G4 G3_P_G4.htseq_count.txt GLD4_KO G3 Polysomal > > GLD4_KO_Polysomal > > > > The files are all in a directory called" HTSEQ_COUNT", which is in the > same > > directory I am working in. I have 27 files in this folder. > >> dir("HTSEQ_COUNT/") > > [1] "G1_I_C.htseq_count.txt" "G1_I_G2.htseq_count.txt" > > [3] "G1_I_G4.htseq_count.txt" "G1_NP_C.htseq_count.txt" > > [5] "G1_NP_G2.htseq_count.txt" "G1_NP_G4.htseq_count.txt" > > [7] "G1_P_C.htseq_count.txt" "G1_P_G2.htseq_count.txt" > > [9] "G1_P_G4.htseq_count.txt" "G2_I_C.htseq_count.txt" > > [11] "G2_I_G2.htseq_count.txt" "G2_I_G4.htseq_count.txt" > > [13] "G2_NP_C.htseq_count.txt" "G2_NP_G2.htseq_count.txt" > > [15] "G2_NP_G4.htseq_count.txt" "G2_P_C.htseq_count.txt" > > [17] "G2_P_G2.htseq_count.txt" "G2_P_G4.htseq_count.txt" > > [19] "G3_I_C.htseq_count.txt" "G3_I_G2.htseq_count.txt" > > [21] "G3_I_G4.htseq_count.txt" "G3_NP_C.htseq_count.txt" > > [23] "G3_NP_G2.htseq_count.txt" "G3_NP_G4.htseq_count.txt" > > [25] "G3_P_C.htseq_count.txt" "G3_P_G2.htseq_count.txt" > > [27] "G3_P_G4.htseq_count.txt" > > > > This is the command I am using to create the count data set object. > > > >> newCountDataSetFromHTSeqCount(countTalbe, directory="HTSEQ_COUNT/") > > > > But it keeps spitting this error massage: > > > > Error in `colnames<-`(`*tmp*`, value = 1:27) : > > attempt to set 'colnames' on an object with less than two dimensions > > > > I even tried to reduce the size of the htseqCountTable to only three > > columns, but it still gives the same erorr. > > > > Does anyone have an idea why I get this error? > > > > > > Thanks > > > > Assa > > > > [[alternative HTML version deleted]] > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor@r-project.org > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > > [[alternative HTML version deleted]]