Hi Gaurav.
Note that the FIRMA scores (and expression values, chip effects, etc.) are
stored in the exponentiated (base 2) scale. So, take log2() of them:
> log2(1568)
[1] 10.6
That's much more feasible.
Cheers,
Mark
On 2010-07-22, at 12:10 AM, gaurav bhatti wrote:
> I wanted to reproduce the results of FIRMA paper for the tissue sample
> data set (exon array:HuEx-1_0-st-v2) . I used the ensebl cdf,
> HuEx-1_0-st-v2,U-Ensembl47,G-Affy which I think is the one the authors
> used. Here is the exact code that I used:
>
> library(aroma.affymetrix)
> verbose <- Arguments$getVerbose(-8, timestamp=TRUE)
> chipType <- "HuEx-1_0-st-v2"
> # Getting annotation data files
> cdf <- AffymetrixCdfFile$byChipType(chipType,tags="U-Ensembl47,G-
> Affy")
> # Defining CEL set
> cs <- AffymetrixCelSet$byName("coloncancer", cdf=cdf)
> #Background Adjustment and Normalization
> bc <- RmaBackgroundCorrection(cs, tag="ensemblcancer")
> csBC <- process(bc,verbose=verbose)
> qn <- QuantileNormalization(csBC, typesToUpdate="pm")
> csN <- process(qn, verbose=verbose)
> #Summarization
> plmTr <- ExonRmaPlm(csN, mergeGroups=TRUE)
> fit(plmTr, verbose=verbose)
> CesTr <- getChipEffectSet(plmTr)
> trFit <- extractDataFrame(CesTr,units=NULL,addNames=TRUE)
> #Alternative Splicing Analysis (FIRMA)
> firma <- FirmaModel(plmTr)
> fit(firma, verbose=verbose)
> fs <- getFirmaScores(firma)
> firma <- extractDataFrame(fs,units=NULL,addNames=TRUE)
> rownames(firma) = firma$groupName
> I am getting some FIRMA values as high as 1568 ( for UNR: 2429323). Is
> that even feasible ?
>
> Gaurav Bhatti
>
> --
> 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 with website http://www.aroma-project.org/.
> To post to this group, send email to aroma-affymetrix@googlegroups.com
> To unsubscribe and other options, go to http://www.aroma-project.org/forum/
------------------------------
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
------------------------------
______________________________________________________________________
The information in this email is confidential and intended solely for the
addressee.
You must not disclose, forward, print or use it without the permission of the
sender.
______________________________________________________________________
--
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 with website http://www.aroma-project.org/.
To post to this group, send email to aroma-affymetrix@googlegroups.com
To unsubscribe and other options, go to http://www.aroma-project.org/forum/
