[BioC] creating a newCountDataSet from HTSeq-count

[Wolfgang Huber]

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 at 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
> 
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