[BioC] edge R exactTest output looks odd - PLEASE HELP!
Audra [guest]
guest at bioconductor.org
Sat Dec 28 01:03:27 CET 2013
Hi,
So I have been using edgeR for a while now to look at some differential expression data of snakes at different time points. I can successfully use exactTest and topTags to get results, but instead of putting them in a nice table like the user guide shows it shows them all weird and makes it very difficult to read or even export. Here is what the output of topTags looks like.
> et <- exactTest(d, pair=c("1h","0h"))
> n <- topTags(et, n=20)
> n
Comparison of groups: 0h-1h
logFC
augustus_masked-Contig169-processed-gene-3.0-mRNA-1 transcript Name:"Similar to Hemoglobin subunit alpha-A (Drymarchon corais erebennus)" offset:645 AED:0.11 eAED:0.11 QI:645|1|1|1|1|1|3|423| -2.857196
maker-Contig3276-snap-gene-0.35-mRNA-1 transcript Name:"Similar to Muc2 Mucin-2 (Fragment) (Rattus norvegicus)" offset:0 AED:0.14 eAED:0.14 QI:0|0|0|1|0.4|0.5|26|0| 3.418006
maker-Contig6179-snap-gene-0.61-mRNA-1 transcript Name:"Similar to SARM1 Sterile alpha and TIR motif-containing protein 1 (Homo sapiens)" offset:0 AED:0.05 eAED:0.05 QI:0|0|0|1|0.37|0.44|9|0| 3.176324
maker-Contig3310-augustus-gene-0.46-mRNA-1 transcript Name:"Similar to HSPA8 Heat shock cognate 71 kDa protein (Equus caballus)" offset:0 AED:0.19 eAED:0.19 QI:0|0.45|0.41|1|1|1|12|0| -2.188642
maker-Contig2409-snap-gene-0.119-mRNA-1 transcript Name:"Similar to SLC27A4 Long-chain fatty acid transport protein 4 (Homo sapiens)" offset:0 AED:0.19 eAED:0.19 QI:0|0.83|0.84|0.92|0.58|0.53|13|515| 2.288095
maker-Contig128-snap-gene-5.59-mRNA-1 transcript Name:"Similar to LRP4 Low-density lipoprotein receptor-related protein 4 (Homo sapiens)" offset:0 AED:0.21 eAED:0.22 QI:0|0.73|0.70|0.90|0.83|0.83|31|0| 2.819809
maker-Contig3982-snap-gene-0.32-mRNA-1 transcript Name:"Similar to CECR2 Cat eye syndrome critical region protein 2 (Homo sapiens)" offset:34 AED:0.05 eAED:0.05 QI:34|0.72|0.52|0.89|0.88|0.78|19|1120| 2.603195
maker-Contig6152-augustus-gene-0.24-mRNA-1 transcript Name:"Similar to Traf2 TNF receptor-associated factor 2 (Mus musculus)" offset:0 AED:0.09 eAED:0.09 QI:0|1|1|1|0.75|1|5|942| -2.367034
maker-Contig1788-snap-gene-1.48-mRNA-1 transcript Name:"Similar to SGK2 Serine/threonine-protein kinase Sgk2 (Homo sapiens)" offset:0 AED:0.15 eAED:0.15 QI:0|0.41|0.46|0.61|0.83|0.92|13|1973| -2.613372
maker-Contig10160-pred_gff_snap_masked-gene-0.0-mRNA-1 transcript Name:"Similar to asah2 Neutral ceramidase (Danio rerio)" offset:0 AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|3|0| 1.850303
maker-Contig2092-augustus-gene-1.46-mRNA-1 transcript Name:"Similar to Nrk1 Nicotinamide riboside kinase 1 (Rattus norvegicus)" offset:0 AED:0.20 eAED:0.20 QI:0|0.6|0.66|1|0.6|0.5|6|847| -1.968943
maker-Contig987-augustus-gene-2.79-mRNA-1 transcript Name:"Similar to C9orf46 Transmembrane protein C9orf46 (Homo sapiens)" offset:338 AED:0.03 eAED:0.03 QI:338|1|1|1|0.5|0.8|5|339| -1.790692
maker-Contig3206-pred_gff_snap_masked-gene-0.0-mRNA-1 transcript Name:"Similar to ADAM12 Disintegrin and metalloproteinase domain-containing protein 12 (Homo sapiens)" offset:0 AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|4|0| 2.659047
augustus_masked-Contig3021-processed-gene-0.2-mRNA-1 transcript Name:"Similar to CLDN15 Claudin-15 (Bos taurus)" offset:0 AED:0.22 eAED:0.22 QI:0|0|0|0.83|1|1|6|0| 1.871232
maker-Contig418-snap-gene-2.48-mRNA-1 transcript Name:"Similar to RBM43 RNA-binding protein 43 (Homo sapiens)" offset:699 AED:0.05 eAED:0.05 QI:699|0.4|0.33|0.66|0.6|0.66|6|0| 2.031038
augustus_masked-Contig3728-processed-gene-0.0-mRNA-1 transcript Name:"Similar to AP2S1 AP-2 complex subunit sigma (Bos taurus)" offset:0 AED:0.12 eAED:0.12 QI:0|0|0|0.66|1|1|3|0| -3.499827
maker-Contig1593-snap-gene-0.14-mRNA-1 transcript Name:"Similar to HBEGF Proheparin-binding EGF-like growth factor (Gallus gallus)" offset:302 AED:0.03 eAED:0.03 QI:302|1|1|1|0.6|0.5|6|1693| -2.205585
maker-Contig5017-augustus-gene-0.43-mRNA-1 transcript Name:"Similar to NR4A1 Nuclear receptor subfamily 4 group A member 1 (Canis familiaris)" offset:133 AED:0.16 eAED:0.16 QI:133|0.83|0.85|1|0.83|0.71|7|598| -1.809087
maker-Contig785-augustus-gene-2.125-mRNA-1 transcript Name:"Similar to DYSF Dysferlin (Homo sapiens)" offset:0 AED:0.05 eAED:0.05 QI:0|0.93|0.93|0.93|0.86|0.87|16|399| -4.666795
maker-Contig2173-snap-gene-0.54-mRNA-1 transcript Name:"Similar to ABR Active breakpoint cluster region-related protein (Homo sapiens)" offset:0 AED:0.11 eAED:0.11 QI:0|0|0|1|0.5|0.33|3|0| -2.273639
logCPM
augustus_masked-Contig169-processed-gene-3.0-mRNA-1 transcript Name:"Similar to Hemoglobin subunit alpha-A (Drymarchon corais erebennus)" offset:645 AED:0.11 eAED:0.11 QI:645|1|1|1|1|1|3|423| 6.191152
maker-Contig3276-snap-gene-0.35-mRNA-1 transcript Name:"Similar to Muc2 Mucin-2 (Fragment) (Rattus norvegicus)" offset:0 AED:0.14 eAED:0.14 QI:0|0|0|1|0.4|0.5|26|0| 3.263290
maker-Contig6179-snap-gene-0.61-mRNA-1 transcript Name:"Similar to SARM1 Sterile alpha and TIR motif-containing protein 1 (Homo sapiens)" offset:0 AED:0.05 eAED:0.05 QI:0|0|0|1|0.37|0.44|9|0| 3.391370
maker-Contig3310-augustus-gene-0.46-mRNA-1 transcript Name:"Similar to HSPA8 Heat shock cognate 71 kDa protein (Equus caballus)" offset:0 AED:0.19 eAED:0.19 QI:0|0.45|0.41|1|1|1|12|0| 9.610127
maker-Contig2409-snap-gene-0.119-mRNA-1 transcript Name:"Similar to SLC27A4 Long-chain fatty acid transport protein 4 (Homo sapiens)" offset:0 AED:0.19 eAED:0.19 QI:0|0.83|0.84|0.92|0.58|0.53|13|515| 4.019203
maker-Contig128-snap-gene-5.59-mRNA-1 transcript Name:"Similar to LRP4 Low-density lipoprotein receptor-related protein 4 (Homo sapiens)" offset:0 AED:0.21 eAED:0.22 QI:0|0.73|0.70|0.90|0.83|0.83|31|0| 3.368075
maker-Contig3982-snap-gene-0.32-mRNA-1 transcript Name:"Similar to CECR2 Cat eye syndrome critical region protein 2 (Homo sapiens)" offset:34 AED:0.05 eAED:0.05 QI:34|0.72|0.52|0.89|0.88|0.78|19|1120| 2.521161
maker-Contig6152-augustus-gene-0.24-mRNA-1 transcript Name:"Similar to Traf2 TNF receptor-associated factor 2 (Mus musculus)" offset:0 AED:0.09 eAED:0.09 QI:0|1|1|1|0.75|1|5|942| 5.425554
maker-Contig1788-snap-gene-1.48-mRNA-1 transcript Name:"Similar to SGK2 Serine/threonine-protein kinase Sgk2 (Homo sapiens)" offset:0 AED:0.15 eAED:0.15 QI:0|0.41|0.46|0.61|0.83|0.92|13|1973| 3.540149
maker-Contig10160-pred_gff_snap_masked-gene-0.0-mRNA-1 transcript Name:"Similar to asah2 Neutral ceramidase (Danio rerio)" offset:0 AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|3|0| 3.603789
maker-Contig2092-augustus-gene-1.46-mRNA-1 transcript Name:"Similar to Nrk1 Nicotinamide riboside kinase 1 (Rattus norvegicus)" offset:0 AED:0.20 eAED:0.20 QI:0|0.6|0.66|1|0.6|0.5|6|847| 4.225327
maker-Contig987-augustus-gene-2.79-mRNA-1 transcript Name:"Similar to C9orf46 Transmembrane protein C9orf46 (Homo sapiens)" offset:338 AED:0.03 eAED:0.03 QI:338|1|1|1|0.5|0.8|5|339| 5.989592
maker-Contig3206-pred_gff_snap_masked-gene-0.0-mRNA-1 transcript Name:"Similar to ADAM12 Disintegrin and metalloproteinase domain-containing protein 12 (Homo sapiens)" offset:0 AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|4|0| 3.212799
augustus_masked-Contig3021-processed-gene-0.2-mRNA-1 transcript Name:"Similar to CLDN15 Claudin-15 (Bos taurus)" offset:0 AED:0.22 eAED:0.22 QI:0|0|0|0.83|1|1|6|0| 3.064311
maker-Contig418-snap-gene-2.48-mRNA-1 transcript Name:"Similar to RBM43 RNA-binding protein 43 (Homo sapiens)" offset:699 AED:0.05 eAED:0.05 QI:699|0.4|0.33|0.66|0.6|0.66|6|0| 3.314820
augustus_masked-Contig3728-processed-gene-0.0-mRNA-1 transcript Name:"Similar to AP2S1 AP-2 complex subunit sigma (Bos taurus)" offset:0 AED:0.12 eAED:0.12 QI:0|0|0|0.66|1|1|3|0| 3.597093
maker-Contig1593-snap-gene-0.14-mRNA-1 transcript Name:"Similar to HBEGF Proheparin-binding EGF-like growth factor (Gallus gallus)" offset:302 AED:0.03 eAED:0.03 QI:302|1|1|1|0.6|0.5|6|1693| 5.743097
maker-Contig5017-augustus-gene-0.43-mRNA-1 transcript Name:"Similar to NR4A1 Nuclear receptor subfamily 4 group A member 1 (Canis familiaris)" offset:133 AED:0.16 eAED:0.16 QI:133|0.83|0.85|1|0.83|0.71|7|598| 6.470491
maker-Contig785-augustus-gene-2.125-mRNA-1 transcript Name:"Similar to DYSF Dysferlin (Homo sapiens)" offset:0 AED:0.05 eAED:0.05 QI:0|0.93|0.93|0.93|0.86|0.87|16|399| 2.599136
maker-Contig2173-snap-gene-0.54-mRNA-1 transcript Name:"Similar to ABR Active breakpoint cluster region-related protein (Homo sapiens)" offset:0 AED:0.11 eAED:0.11 QI:0|0|0|1|0.5|0.33|3|0| 3.335853
PValue
augustus_masked-Contig169-processed-gene-3.0-mRNA-1 transcript Name:"Similar to Hemoglobin subunit alpha-A (Drymarchon corais erebennus)" offset:645 AED:0.11 eAED:0.11 QI:645|1|1|1|1|1|3|423| 3.298254e-05
maker-Contig3276-snap-gene-0.35-mRNA-1 transcript Name:"Similar to Muc2 Mucin-2 (Fragment) (Rattus norvegicus)" offset:0 AED:0.14 eAED:0.14 QI:0|0|0|1|0.4|0.5|26|0| 3.877782e-05
maker-Contig6179-snap-gene-0.61-mRNA-1 transcript Name:"Similar to SARM1 Sterile alpha and TIR motif-containing protein 1 (Homo sapiens)" offset:0 AED:0.05 eAED:0.05 QI:0|0|0|1|0.37|0.44|9|0| 5.106264e-05
maker-Contig3310-augustus-gene-0.46-mRNA-1 transcript Name:"Similar to HSPA8 Heat shock cognate 71 kDa protein (Equus caballus)" offset:0 AED:0.19 eAED:0.19 QI:0|0.45|0.41|1|1|1|12|0| 5.891387e-05
maker-Contig2409-snap-gene-0.119-mRNA-1 transcript Name:"Similar to SLC27A4 Long-chain fatty acid transport protein 4 (Homo sapiens)" offset:0 AED:0.19 eAED:0.19 QI:0|0.83|0.84|0.92|0.58|0.53|13|515| 1.388640e-04
maker-Contig128-snap-gene-5.59-mRNA-1 transcript Name:"Similar to LRP4 Low-density lipoprotein receptor-related protein 4 (Homo sapiens)" offset:0 AED:0.21 eAED:0.22 QI:0|0.73|0.70|0.90|0.83|0.83|31|0| 2.155298e-04
maker-Contig3982-snap-gene-0.32-mRNA-1 transcript Name:"Similar to CECR2 Cat eye syndrome critical region protein 2 (Homo sapiens)" offset:34 AED:0.05 eAED:0.05 QI:34|0.72|0.52|0.89|0.88|0.78|19|1120| 5.390950e-04
maker-Contig6152-augustus-gene-0.24-mRNA-1 transcript Name:"Similar to Traf2 TNF receptor-associated factor 2 (Mus musculus)" offset:0 AED:0.09 eAED:0.09 QI:0|1|1|1|0.75|1|5|942| 1.062257e-03
maker-Contig1788-snap-gene-1.48-mRNA-1 transcript Name:"Similar to SGK2 Serine/threonine-protein kinase Sgk2 (Homo sapiens)" offset:0 AED:0.15 eAED:0.15 QI:0|0.41|0.46|0.61|0.83|0.92|13|1973| 1.417311e-03
maker-Contig10160-pred_gff_snap_masked-gene-0.0-mRNA-1 transcript Name:"Similar to asah2 Neutral ceramidase (Danio rerio)" offset:0 AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|3|0| 3.340976e-03
maker-Contig2092-augustus-gene-1.46-mRNA-1 transcript Name:"Similar to Nrk1 Nicotinamide riboside kinase 1 (Rattus norvegicus)" offset:0 AED:0.20 eAED:0.20 QI:0|0.6|0.66|1|0.6|0.5|6|847| 3.350736e-03
maker-Contig987-augustus-gene-2.79-mRNA-1 transcript Name:"Similar to C9orf46 Transmembrane protein C9orf46 (Homo sapiens)" offset:338 AED:0.03 eAED:0.03 QI:338|1|1|1|0.5|0.8|5|339| 3.837191e-03
maker-Contig3206-pred_gff_snap_masked-gene-0.0-mRNA-1 transcript Name:"Similar to ADAM12 Disintegrin and metalloproteinase domain-containing protein 12 (Homo sapiens)" offset:0 AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|4|0| 3.898098e-03
augustus_masked-Contig3021-processed-gene-0.2-mRNA-1 transcript Name:"Similar to CLDN15 Claudin-15 (Bos taurus)" offset:0 AED:0.22 eAED:0.22 QI:0|0|0|0.83|1|1|6|0| 3.944978e-03
maker-Contig418-snap-gene-2.48-mRNA-1 transcript Name:"Similar to RBM43 RNA-binding protein 43 (Homo sapiens)" offset:699 AED:0.05 eAED:0.05 QI:699|0.4|0.33|0.66|0.6|0.66|6|0| 4.279215e-03
augustus_masked-Contig3728-processed-gene-0.0-mRNA-1 transcript Name:"Similar to AP2S1 AP-2 complex subunit sigma (Bos taurus)" offset:0 AED:0.12 eAED:0.12 QI:0|0|0|0.66|1|1|3|0| 4.889554e-03
maker-Contig1593-snap-gene-0.14-mRNA-1 transcript Name:"Similar to HBEGF Proheparin-binding EGF-like growth factor (Gallus gallus)" offset:302 AED:0.03 eAED:0.03 QI:302|1|1|1|0.6|0.5|6|1693| 5.249437e-03
maker-Contig5017-augustus-gene-0.43-mRNA-1 transcript Name:"Similar to NR4A1 Nuclear receptor subfamily 4 group A member 1 (Canis familiaris)" offset:133 AED:0.16 eAED:0.16 QI:133|0.83|0.85|1|0.83|0.71|7|598| 5.262003e-03
maker-Contig785-augustus-gene-2.125-mRNA-1 transcript Name:"Similar to DYSF Dysferlin (Homo sapiens)" offset:0 AED:0.05 eAED:0.05 QI:0|0.93|0.93|0.93|0.86|0.87|16|399| 5.400893e-03
maker-Contig2173-snap-gene-0.54-mRNA-1 transcript Name:"Similar to ABR Active breakpoint cluster region-related protein (Homo sapiens)" offset:0 AED:0.11 eAED:0.11 QI:0|0|0|1|0.5|0.33|3|0| 5.521102e-03
FDR
augustus_masked-Contig169-processed-gene-3.0-mRNA-1 transcript Name:"Similar to Hemoglobin subunit alpha-A (Drymarchon corais erebennus)" offset:645 AED:0.11 eAED:0.11 QI:645|1|1|1|1|1|3|423| 0.3738821
maker-Contig3276-snap-gene-0.35-mRNA-1 transcript Name:"Similar to Muc2 Mucin-2 (Fragment) (Rattus norvegicus)" offset:0 AED:0.14 eAED:0.14 QI:0|0|0|1|0.4|0.5|26|0| 0.3738821
maker-Contig6179-snap-gene-0.61-mRNA-1 transcript Name:"Similar to SARM1 Sterile alpha and TIR motif-containing protein 1 (Homo sapiens)" offset:0 AED:0.05 eAED:0.05 QI:0|0|0|1|0.37|0.44|9|0| 0.3738821
maker-Contig3310-augustus-gene-0.46-mRNA-1 transcript Name:"Similar to HSPA8 Heat shock cognate 71 kDa protein (Equus caballus)" offset:0 AED:0.19 eAED:0.19 QI:0|0.45|0.41|1|1|1|12|0| 0.3738821
maker-Contig2409-snap-gene-0.119-mRNA-1 transcript Name:"Similar to SLC27A4 Long-chain fatty acid transport protein 4 (Homo sapiens)" offset:0 AED:0.19 eAED:0.19 QI:0|0.83|0.84|0.92|0.58|0.53|13|515| 0.7050126
maker-Contig128-snap-gene-5.59-mRNA-1 transcript Name:"Similar to LRP4 Low-density lipoprotein receptor-related protein 4 (Homo sapiens)" offset:0 AED:0.21 eAED:0.22 QI:0|0.73|0.70|0.90|0.83|0.83|31|0| 0.9118705
maker-Contig3982-snap-gene-0.32-mRNA-1 transcript Name:"Similar to CECR2 Cat eye syndrome critical region protein 2 (Homo sapiens)" offset:34 AED:0.05 eAED:0.05 QI:34|0.72|0.52|0.89|0.88|0.78|19|1120| 1.0000000
maker-Contig6152-augustus-gene-0.24-mRNA-1 transcript Name:"Similar to Traf2 TNF receptor-associated factor 2 (Mus musculus)" offset:0 AED:0.09 eAED:0.09 QI:0|1|1|1|0.75|1|5|942| 1.0000000
maker-Contig1788-snap-gene-1.48-mRNA-1 transcript Name:"Similar to SGK2 Serine/threonine-protein kinase Sgk2 (Homo sapiens)" offset:0 AED:0.15 eAED:0.15 QI:0|0.41|0.46|0.61|0.83|0.92|13|1973| 1.0000000
maker-Contig10160-pred_gff_snap_masked-gene-0.0-mRNA-1 transcript Name:"Similar to asah2 Neutral ceramidase (Danio rerio)" offset:0 AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|3|0| 1.0000000
maker-Contig2092-augustus-gene-1.46-mRNA-1 transcript Name:"Similar to Nrk1 Nicotinamide riboside kinase 1 (Rattus norvegicus)" offset:0 AED:0.20 eAED:0.20 QI:0|0.6|0.66|1|0.6|0.5|6|847| 1.0000000
maker-Contig987-augustus-gene-2.79-mRNA-1 transcript Name:"Similar to C9orf46 Transmembrane protein C9orf46 (Homo sapiens)" offset:338 AED:0.03 eAED:0.03 QI:338|1|1|1|0.5|0.8|5|339| 1.0000000
maker-Contig3206-pred_gff_snap_masked-gene-0.0-mRNA-1 transcript Name:"Similar to ADAM12 Disintegrin and metalloproteinase domain-containing protein 12 (Homo sapiens)" offset:0 AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|4|0| 1.0000000
augustus_masked-Contig3021-processed-gene-0.2-mRNA-1 transcript Name:"Similar to CLDN15 Claudin-15 (Bos taurus)" offset:0 AED:0.22 eAED:0.22 QI:0|0|0|0.83|1|1|6|0| 1.0000000
maker-Contig418-snap-gene-2.48-mRNA-1 transcript Name:"Similar to RBM43 RNA-binding protein 43 (Homo sapiens)" offset:699 AED:0.05 eAED:0.05 QI:699|0.4|0.33|0.66|0.6|0.66|6|0| 1.0000000
augustus_masked-Contig3728-processed-gene-0.0-mRNA-1 transcript Name:"Similar to AP2S1 AP-2 complex subunit sigma (Bos taurus)" offset:0 AED:0.12 eAED:0.12 QI:0|0|0|0.66|1|1|3|0| 1.0000000
maker-Contig1593-snap-gene-0.14-mRNA-1 transcript Name:"Similar to HBEGF Proheparin-binding EGF-like growth factor (Gallus gallus)" offset:302 AED:0.03 eAED:0.03 QI:302|1|1|1|0.6|0.5|6|1693| 1.0000000
maker-Contig5017-augustus-gene-0.43-mRNA-1 transcript Name:"Similar to NR4A1 Nuclear receptor subfamily 4 group A member 1 (Canis familiaris)" offset:133 AED:0.16 eAED:0.16 QI:133|0.83|0.85|1|0.83|0.71|7|598| 1.0000000
maker-Contig785-augustus-gene-2.125-mRNA-1 transcript Name:"Similar to DYSF Dysferlin (Homo sapiens)" offset:0 AED:0.05 eAED:0.05 QI:0|0.93|0.93|0.93|0.86|0.87|16|399| 1.0000000
maker-Contig2173-snap-gene-0.54-mRNA-1 transcript Name:"Similar to ABR Active breakpoint cluster region-related protein (Homo sapiens)" offset:0 AED:0.11 eAED:0.11 QI:0|0|0|1|0.5|0.33|3|0| 1.0000000
How do you get that nice table format everyone shows. I am getting frustrated because i can generate data so easily, but I just cannot get it into a format to look at it easily. Any input would be greatly appreciated.
Audra
-- output of sessionInfo():
R version 3.0.2 (2013-09-25)
Platform: x86_64-apple-darwin10.8.0 (64-bit)
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] edgeR_3.4.2 limma_3.18.6
loaded via a namespace (and not attached):
[1] tools_3.0.2
--
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