Re: [galaxy-user] Help!!! cuffdiff log2 value
Hi Jiwen, As far as I know, this is possible. The CuffDiff log2 value is defined here: http://cufflinks.cbcb.umd.edu/manual.html#gene_exp_diff 7 FPKMx 8.01089 FPKM of the gene in sample x 8 FPKMy 8.551545 FPKM of the gene in sample y 9 log2(FPKMy/FPKMx) 0.06531 The (base 2) log of the fold change y/x And log(2) in general (including a graph, which can help with visualizing) is described here (although the web is full if similar): http://en.wikipedia.org/wiki/Logarithm I can see that this same Q on seqanswers.com recieved pretty much the same answer (in brief! http://seqanswers.com/forums/showthread.php?t=19558), so I think you are safe using the data as it as generated. Taking a look at the inputs would be advised if the results were unexpected. If you do still have concerns about the log(2) calculation, asking the tool authors directly (if you have't done so already) at tophat.cuffli...@gmail.com is always an option, to tripple check. Best, Jen Galaxy team On 4/26/12 7:48 AM, 杨继文 wrote: Hi, I am analyzing my RNA-Seq data. After running cuffdiff, I got a list of differentially expressed transcrpts or genes. As far as I know, log2 value = fold change. However, there are minus values. Is this possible?? log2 value can not be minus. Did I miss something?? Looking forward to your help. Thanks in advance. Best Jiwen 网易Lofter，专注兴趣，分享创作！ http://www.lofter.com ___ 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/ -- Jennifer Jackson http://galaxyproject.org ___ 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] Help!!! cuffdiff log2 value
I think the sign is to show if it is x-fold more than the first condition (+) or x-fold less than the first condition (-). A regular fold would give you values from 1-whatever if sample 2 is more than sample 1, and a fraction (0-1) if sample 1 is expressed more than sample 2. The log lets you get both on the same scale, so that 2 means (on log2 scale) four-fold upregulated, and -2 means four-fold downregulated. FPKM x FPKM y y/x log(y/x) 1 2 2 1 1 0.5 0.5 -1 On 10/05/2012 19:00, Jennifer Jackson wrote: Hi Jiwen, As far as I know, this is possible. The CuffDiff log2 value is defined here: http://cufflinks.cbcb.umd.edu/manual.html#gene_exp_diff 7 FPKMx 8.01089 FPKM of the gene in sample x 8 FPKMy 8.551545 FPKM of the gene in sample y 9 log2(FPKMy/FPKMx) 0.06531 The (base 2) log of the fold change y/x And log(2) in general (including a graph, which can help with visualizing) is described here (although the web is full if similar): http://en.wikipedia.org/wiki/Logarithm I can see that this same Q on seqanswers.com recieved pretty much the same answer (in brief! http://seqanswers.com/forums/showthread.php?t=19558), so I think you are safe using the data as it as generated. Taking a look at the inputs would be advised if the results were unexpected. If you do still have concerns about the log(2) calculation, asking the tool authors directly (if you have't done so already) at tophat.cuffli...@gmail.com is always an option, to tripple check. Best, Jen Galaxy team On 4/26/12 7:48 AM, 杨继文 wrote: Hi, I am analyzing my RNA-Seq data. After running cuffdiff, I got a list of differentially expressed transcrpts or genes. As far as I know, log2 value = fold change. However, there are minus values. Is this possible?? log2 value can not be minus. Did I miss something?? Looking forward to your help. Thanks in advance. Best Jiwen 网易Lofter，专注兴趣，分享创作！ http://www.lofter.com ___ 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] Help!!! cuffdiff log2 value
Hi Noa, This is it exactly - thanks for adding in the interpretation! Jen On 5/10/12 11:54 AM, Noa Sher wrote: I think the sign is to show if it is x-fold more than the first condition (+) or x-fold less than the first condition (-). A regular fold would give you values from 1-whatever if sample 2 is more than sample 1, and a fraction (0-1) if sample 1 is expressed more than sample 2. The log lets you get both on the same scale, so that 2 means (on log2 scale) four-fold upregulated, and -2 means four-fold downregulated. FPKM x FPKM y y/x log(y/x) 1 2 2 1 1 0.5 0.5 -1 On 10/05/2012 19:00, Jennifer Jackson wrote: Hi Jiwen, As far as I know, this is possible. The CuffDiff log2 value is defined here: http://cufflinks.cbcb.umd.edu/manual.html#gene_exp_diff 7 FPKMx 8.01089 FPKM of the gene in sample x 8 FPKMy 8.551545 FPKM of the gene in sample y 9 log2(FPKMy/FPKMx) 0.06531 The (base 2) log of the fold change y/x And log(2) in general (including a graph, which can help with visualizing) is described here (although the web is full if similar): http://en.wikipedia.org/wiki/Logarithm I can see that this same Q on seqanswers.com recieved pretty much the same answer (in brief! http://seqanswers.com/forums/showthread.php?t=19558), so I think you are safe using the data as it as generated. Taking a look at the inputs would be advised if the results were unexpected. If you do still have concerns about the log(2) calculation, asking the tool authors directly (if you have't done so already) at tophat.cuffli...@gmail.com is always an option, to tripple check. Best, Jen Galaxy team On 4/26/12 7:48 AM, 杨继文 wrote: Hi, I am analyzing my RNA-Seq data. After running cuffdiff, I got a list of differentially expressed transcrpts or genes. As far as I know, log2 value = fold change. However, there are minus values. Is this possible?? log2 value can not be minus. Did I miss something?? Looking forward to your help. Thanks in advance. Best Jiwen 网易Lofter，专注兴趣，分享创作！ http://www.lofter.com ___ 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/ -- Jennifer Jackson http://galaxyproject.org ___ 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/
