Hi Hailei. This has been discussed before as well. You might start with:
http://groups.google.com/group/aroma-affymetrix/browse_thread/thread/36d8c59d742fc503/ http://groups.google.com/group/aroma-affymetrix/browse_thread/thread/f4d015cae1848f51/ You should definitely take log2 before proceeding with FIRMA scores. Since they are a summary of residuals for a probeset (see the paper for details), you will have positive and negative numbers. Cheers, Mark On 17-Oct-09, at 3:46 AM, hailei....@gmail.com wrote: > > Dear All, > > I have 2 tumor samples and 2 control samples and want to find > alternative splicing. > > After I got the FIRMA score, Could I use limma to find the alternative > splicing? > > Before using limma, I did log2 scale to FIRMA score. But I found there > are a lot of negative value in data set. It is common? > > Original Firma score: > head(exFirma) > unitName groupName unit group cell RD2009092839 RD2009092840 > RD2009092841 > 1 6838637 4304927 1 1 1 0.4586444 0.2794902 > 1.8639828 > 2 6838637 4330595 1 2 2 0.6102609 0.9152724 > 1.3151890 > 3 6838637 4356771 1 3 3 1.6570473 0.1941053 > 1.3088931 > 4 6838637 4366326 1 4 4 0.7417230 1.8255262 > 0.7095107 > 5 6838637 4367951 1 5 5 1.0001453 1.3591065 > 0.6875097 > 6 6838637 4396376 1 6 6 1.4089704 0.4405679 > 1.1440083 > RD2009092842 > 1 1.3710542 > 2 1.3612753 > 3 0.8766123 > 4 0.6292946 > 5 1.2785655 > 6 0.6761603 > > log2 score: >> head(exFirma) > unitName groupName unit group cell RD2009092839 RD2009092840 > RD2009092841 > 1 6838637 4304927 1 1 1 -1.1245521013 -1.8391304 > 0.8983885 > 2 6838637 4330595 1 2 2 -0.7125019273 -0.1277269 > 0.3952701 > 3 6838637 4356771 1 3 3 0.7286147599 -2.3650883 > 0.3883473 > 4 6838637 4366326 1 4 4 -0.4310475869 0.8683124 > -0.4951036 > 5 6838637 4367951 1 5 5 0.0002096316 0.4426586 > -0.5405480 > 6 6838637 4396376 1 6 6 0.4946412584 -1.1825638 > 0.1940975 > RD2009092842 > 1 0.4552856 > 2 0.4449589 > 3 -0.1899892 > 4 -0.6681926 > 5 0.3545261 > 6 -0.5645628 > > Thanks > > Hailei > > ------------------------------ Mark Robinson, PhD (Melb) Epigenetics Laboratory, Garvan Bioinformatics Division, WEHI e: m.robin...@garvan.org.au e: mrobin...@wehi.edu.au p: +61 (0)3 9345 2628 f: +61 (0)3 9347 0852 ------------------------------ --~--~---------~--~----~------------~-------~--~----~ When reporting problems on aroma.affymetrix, make sure 1) to run the latest version of the package, 2) to report the output of sessionInfo() and traceback(), and 3) to post a complete code example. You received this message because you are subscribed to the Google Groups "aroma.affymetrix" group. To post to this group, send email to aroma-affymetrix@googlegroups.com To unsubscribe from this group, send email to aroma-affymetrix-unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/aroma-affymetrix?hl=en -~----------~----~----~----~------~----~------~--~---
