EdgeR DESeq2 errors

Question: EdgeR DESeq2 errors

10 weeks ago by

mbt • 0

mbt • 0 wrote:

Hi Finally at the point of doing some differential expression analysis

I used HTseq2 to align my data to mm10. That was successful. I used the " Back to Unnamed history htseq-count on collection 316" file and the corresponding mate file i.e treated group. In both cases when I fed the data into DEseq2 or EdgeR I get error. The file is highlighted in red. In the case of EdgeR I get the following Error

Fatal error: Exit code 1 ()
Error in `row.names<-.data.frame`(`*tmp*`, value = c("X0", "X0", "X0",  : 
  duplicate 'row.names' are not allowed
Calls: row.names<- -> row.names<-.data.frame
Warning message:
non-unique value when setting 'row.names': ‘X0’

Here are the first couple lines from of text output from the HTseq feature file for one of the replicates

00R_AC107638.2  0
00R_Pgap2   0
0610009O20Rik   1020
1110020A21Rik   18
1110036E04Rik   0
1600014C23Rik   3
1600017P15Rik   0
1700015F17Rik   1
1700018M17Rik   0
1700022N22Rik   4
1700024J04Rik   0
1700028P14Rik   0
1700037F24Rik   0
1700067P10Rik   0
1700086O06Rik   60
1700123K08Rik   0
1810049J17Rik   3
1810055G02Rik   1051
19.47525802-47711187.1  0
2.145048962-146444327.1 0
2010001E11Rik   0
2010003K11Rik   1
2010015M23Rik   4
2010110K18Rik   14
2010300F17Rik   82
2210008F06Rik   14
2310026I22Rik   0
2310031A07Rik   2
2310039H08Rik   254
2410015M20Rik   1081
2410024N13Rik   0
2610020F03Rik   0
2700012I20Rik   4
2700016F22Rik   3
2700046G09Rik   16
2700062C07Rik   273
2810403A07Rik   1320
2810425M01Rik   1
2900055J20Rik   0
3100002H09Rik   0
3110018I06Rik   0
3110021N24Rik   3
3110070M22Rik   1
3110082I17Rik   271
4732491K20Rik   41
4831440E17Rik   2
4833407H14Rik   0
4833418N17Rik   0
4921501E09Rik   0
4921524L21Rik   0
4930426L09Rik   4
4930442H23Rik   1
4930444M15Rik   1
4930445N18Rik   3
4930455D15Rik   1
4930465K10Rik   1
4930480K23Rik   19
4930505N22Rik   1
4930507D05Rik   4
4930515G13Rik   0
4930518I15Rik   0
4930519P11Rik   0
4930524J08Rik   16
4930535I16Rik   0
4930546C10Rik   0
4930552P12Rik   3
4930553M12Rik   0
4930563E18Rik   0
4930583I09Rik   0
4930598A11Rik   0
4931403G20Rik   0
4931409K22Rik   1
4931440J10Rik   1
4932430I15Rik   0
4933412A08Rik   0
4933415A04Rik   0
4933427I04Rik   0
5031415H12Rik   9
5330417H12Rik   0
5730596B20Rik   0
5930422O12Rik   0
6030445D17Rik   23
6030452D12Rik   0
6330403N20Rik   0
6530411M01Rik   0
8030462N17Rik   603
9.104944562-105295281.1 0
9030612E09Rik   53
9130008F23Rik   36
9130011E15Rik   733
9130213A22Rik   10
930412E21Rik    0
9330132A10Rik   0
9330136K24Rik   5
9330161L09Rik   6
9430025C20Rik   1
9430097D07Rik   1
9430098F02Rik   0
9530027J09Rik   2
9830107B12Rik   0
9930104L06Rik   97
9930111J21Rik1  71
9930111J21Rik2  329
A130006I12Rik   4
A1bg    0
A1cf    0
A230072I06Rik   0
A2m 0
A330032B11Rik   0
A330069E16Rik   19
A330094K24Rik   0
A3galt2 4
A430046D13Rik   79
A4galt  968
A4gnt   2
A530064D06Rik   0
A530084C06Rik   14
A630075F10Rik   0
A730015C16Rik   1
A730061H03Rik   0
A730071L15Rik   1
A830052D11Rik   2
A930002H24Rik   14
A930007I19Rik   10
A930024N18Rik   0
A930035D04Rik   27
AA543186    13
AC012382.1  2
AC012382.2  0
AC015800.4  44
AC021667.1  0
AC025622.3  2
AC026231.3  1
AC026478.1  12764
AC027285.1  0
AC034099.1  0
AC068006.3  0
AC068006.4  0

Is there a formatting issue? Is there someway to curate the data prior to piping into DESeq2/EdgeR

Mike

rna-seq de deseq2 edger • 132 views

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modified 10 weeks ago by Jennifer Hillman Jackson ♦ 25k • written 10 weeks ago by mbt • 0

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