Assa Yeroslaviz | 10 Oct 16:03 2013
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Re: creating a newCountDataSet from HTSeq-count

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@...> 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@...> 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]]
> >
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