[aroma.affymetrix] how to analysis the FIRMA score

2009-11-19 Thread camelbbs
Hi, After I got the firma scores, how can i analyze it. I see boxplot of firma scores in the paper. So how i can get the same result. I want to check the alternative splicing between our several samples. Now I have got the score of each one but How to compare them. Thanks very much. Jiang -- Wh

[aroma.affymetrix] Re: FIRMAGene with masked CEL files

2009-11-19 Thread camelbbs
Hi Mark, I want to ask how to construct custom CDF and how to replace it in CEL files. Thanks, Best, Jiang On Nov 16, 7:18 pm, Mark Robinson wrote: > Hi Tim. > > The FIRMAGene code is not designed to play nice with NAs in the probe   > level data.  I'm somewhat hesitant to include this because it

Re: extracting FIRMA scores (Was: [aroma.affymetrix] a question)

2009-11-19 Thread camelbbs
Thanks very much. But what does the FIRMA score mean if it didn't compare the different samples. Best, Jiang On Nov 17, 5:54 pm, Mark Robinson wrote: > Hi Jiang. > > Its helpful to use meaningful subject headers, so that others can   > search the mailing lists.  So, I've changed your messages to

[aroma.affymetrix] Creat a CnChipEffect set from CnChipEffectFile / calculateBaseline vs getAverageFile

2009-11-19 Thread marco
Dear Herink, I have 2 technical questions (I saw something similar regarding older versions). I generated a cesN set, extracted some arrays that I want to average: ### cesA <- extract(cesN, c(1:2)) cesEX <- extract(cesN, c(7:9)) sc364 <- calculateBaseline(cesEX, chromosomes=1:23, ploidy=2,defa