edge R exactTest output looks odd - PLEASE HELP!
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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 -- Sent via the guest posting facility at bioconductor.org.
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Reema Singh ▴ 570
@reema-singh-4373
Last seen 9.6 years ago
Hi Audra, Your row names of your tables are very long,which disrupt the formatting of your table. When you generate count table at that time, keep your row names (gene names) small and then try. I hope this will works. Regards On Sat, Dec 28, 2013 at 5:33 AM, Audra [guest] <guest@bioconductor.org>wrote: > > 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 > > -- > Sent via the guest posting facility at bioconductor.org. > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > -- Reema Singh Postdoctoral Research Assistant College of Life Sciences University of Dundee, Dundee DD1 4HN, Scotland United Kingdom [[alternative HTML version deleted]]
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