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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