[galaxy-user] Question about output CuffDiff SplicingDiff
Hi there, Looking at the output of the SplicingDiff files of CuffDiff, me and my colleagues are preplexed about the output of the p_values and q_values. We've tried different inputs of different samples to compare but never seem to manage to get p_values smaller than 0.50 and we keep getting higher than 1 q_values (also smaller which we expect) which we think is strange too. The input files we use for the CuffDiff are the CuffCompare of a combined CuffCompare of a dataset, or the CuffCompare of just the two samples we want to analyse. For the samples input files we use the TopHat files respectively. Could you please help us get meaningful results for the SplicingDiff files or help us understand the data? The top 5 rows of our typical SplicingDiff file: test_id gene_id genelocus sample_1 sample_2 1583 TSS11905 XLOC_028193- chr5:134910259-134914719 q1 q2 2385 TSS12870 XLOC_030892- chr7:29976178-30008608 q1 q2 8005 TSS6887 XLOC_016656- chr18:47803031-47807892 q1 q2 10214 TSS9761 XLOC_022527- chr20:43128822-43138649 q1 q2 2818 TSS13383 XLOC_032450- chr8:100899717-100905900 q1 q2 status value_1 value_2sqrt.JS. test_stat p_value q_value 1583 OK 0 0 0.000771867 0.797878 0.501645 164.5400 2385 OK 0 0 0.001548470 0.797809 0.505482 82.8991 8005 OK 0 0 0.003288510 0.797717 0.508184 55.5615 10214 OK 0 0 0.001414180 0.797620 0.510277 41.8427 2818 OK 0 0 0.007112780 0.797416 0.513678 33.6973 Thanks in advance for your most appreciated help, Felix Mayr ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-user] Question about output CuffDiff SplicingDiff
Felix, You seem to be providing the correct inputs to Cuffdiff and it appears to be producing valid output. More information about setting parameter values and interpreting Cuffdiff can be found in manual: http://cufflinks.cbcb.umd.edu/manual.html#cuffdiff Good luck, J. On Jun 16, 2011, at 8:13 AM, Felix Mayr wrote: Hi there, Looking at the output of the SplicingDiff files of CuffDiff, me and my colleagues are preplexed about the output of the p_values and q_values. We've tried different inputs of different samples to compare but never seem to manage to get p_values smaller than 0.50 and we keep getting higher than 1 q_values (also smaller which we expect) which we think is strange too. The input files we use for the CuffDiff are the CuffCompare of a combined CuffCompare of a dataset, or the CuffCompare of just the two samples we want to analyse. For the samples input files we use the TopHat files respectively. Could you please help us get meaningful results for the SplicingDiff files or help us understand the data? The top 5 rows of our typical SplicingDiff file: test_id gene_id genelocus sample_1 sample_2 1583 TSS11905 XLOC_028193- chr5:134910259-134914719 q1 q2 2385 TSS12870 XLOC_030892- chr7:29976178-30008608 q1 q2 8005 TSS6887 XLOC_016656- chr18:47803031-47807892 q1 q2 10214 TSS9761 XLOC_022527- chr20:43128822-43138649 q1 q2 2818 TSS13383 XLOC_032450- chr8:100899717-100905900 q1 q2 status value_1 value_2sqrt.JS. test_stat p_value q_value 1583 OK 0 0 0.000771867 0.797878 0.501645 164.5400 2385 OK 0 0 0.001548470 0.797809 0.505482 82.8991 8005 OK 0 0 0.003288510 0.797717 0.508184 55.5615 10214 OK 0 0 0.001414180 0.797620 0.510277 41.8427 2818 OK 0 0 0.007112780 0.797416 0.513678 33.6973 Thanks in advance for your most appreciated help, Felix Mayr ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-user] Question about output CuffDiff SplicingDiff
What version of Cufflinks is your Galaxy installation running? A recent version (1.00 and 1.01) had a problem that was causing the splicing and promoter use tests to have very few differentially regulated genes, according to http://cufflinks.cbcb.umd.edu/. -rory On Jun 16, 2011, at 8:13 AM, Felix Mayr wrote: Hi there, Looking at the output of the SplicingDiff files of CuffDiff, me and my colleagues are preplexed about the output of the p_values and q_values. We've tried different inputs of different samples to compare but never seem to manage to get p_values smaller than 0.50 and we keep getting higher than 1 q_values (also smaller which we expect) which we think is strange too. The input files we use for the CuffDiff are the CuffCompare of a combined CuffCompare of a dataset, or the CuffCompare of just the two samples we want to analyse. For the samples input files we use the TopHat files respectively. Could you please help us get meaningful results for the SplicingDiff files or help us understand the data? The top 5 rows of our typical SplicingDiff file: test_id gene_id genelocus sample_1 sample_2 1583 TSS11905 XLOC_028193- chr5:134910259-134914719 q1 q2 2385 TSS12870 XLOC_030892- chr7:29976178-30008608 q1 q2 8005 TSS6887 XLOC_016656- chr18:47803031-47807892 q1 q2 10214 TSS9761 XLOC_022527- chr20:43128822-43138649 q1 q2 2818 TSS13383 XLOC_032450- chr8:100899717-100905900 q1 q2 status value_1 value_2sqrt.JS. test_stat p_value q_value 1583 OK 0 0 0.000771867 0.797878 0.501645 164.5400 2385 OK 0 0 0.001548470 0.797809 0.505482 82.8991 8005 OK 0 0 0.003288510 0.797717 0.508184 55.5615 10214 OK 0 0 0.001414180 0.797620 0.510277 41.8427 2818 OK 0 0 0.007112780 0.797416 0.513678 33.6973 Thanks in advance for your most appreciated help, Felix Mayr ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
