Re: [galaxy-user] cuffdiff values different for same sample
Hello, Thank you for sharing your history. The difference in FPKM values can be explained by the use of the -N option (Perform quartile normalization: Yes). Set this to No to avoid the variable per-run normalization. This has also been discussed at seqanswers.com: http://seqanswers.com/forums/showthread.php?t=4606 Hopefully this helps! Jen Galaxy team On 10/12/12 9:43 AM, i b wrote: Hello forum, I have ran cuffdiff with two samples, treated vs untreated, and had certain values as expressed in the output (isoform differential expression). When I ran it again, using a different treated sample, but SAME UNTREATED SAMPLE, the values assigned to the untreated are different. Why is this if values are calculated from a unique FPKM? This happend for other jobs where I have ran the same untreated vs other treated samples... Thanks a lot, ib ___ 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] cuffdiff values different for same sample
Hello, Would you be able to share a history containing these data? Use Options (gear icon) - Share or Publish, generate the share link, then copy and paste that into a reply email sent to me directly. Please note the dataset #'s for the Cuffdiff runs that you are comparing and make sure that all inputs are undeleted. Best, Jen Galaxy team On 10/12/12 9:43 AM, i b wrote: Hello forum, I have ran cuffdiff with two samples, treated vs untreated, and had certain values as expressed in the output (isoform differential expression). When I ran it again, using a different treated sample, but SAME UNTREATED SAMPLE, the values assigned to the untreated are different. Why is this if values are calculated from a unique FPKM? This happend for other jobs where I have ran the same untreated vs other treated samples... Thanks a lot, ib ___ 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/
[galaxy-user] cuffdiff values different for same sample
Hello forum, I have ran cuffdiff with two samples, treated vs untreated, and had certain values as expressed in the output (isoform differential expression). When I ran it again, using a different treated sample, but SAME UNTREATED SAMPLE, the values assigned to the untreated are different. Why is this if values are calculated from a unique FPKM? This happend for other jobs where I have ran the same untreated vs other treated samples... Thanks a lot, ib ___ 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/
