I am looking for some help in doing the FIRMA script output I
got..Hopefully one of you will be able to help. We used the scripts
outlined in the vignette
( http://www.biomedcentral.com/content/supplementary/gm248-S1.PDF) to do
firma analysis. The script used is given below:
--------------------------------------------------------------------------------------------------------------------------------------------------------------------
chipType <- "HuEx-1_0-st-v2"
cdf <- AffymetrixCdfFile$byChipType(chipType, tags="coreR3,A20071112,EP")
print(cdf)
cs <- AffymetrixCelSet$byName("NIK_2014", cdf=cdf)
print(cs)
setCdf(cs, cdf)
bc <- RmaBackgroundCorrection(cs, tags="*,coreR3")
csBC <- process(bc,verbose=verbose)
qn <- QuantileNormalization(csBC, typesToUpdate="pm")
csN <- process(qn, verbose=verbose)
plmTr <- ExonRmaPlm(csN, mergeGroups=TRUE)
fit(plmTr, verbose=verbose)
rs <- calculateResidualSet(plmTr, verbose=verbose) #this is the quality
assessment of the PLM fit.
cesTr <- getChipEffectSet(plmTr)
trFit <- extractDataFrame(cesTr, units=1:3, addNames=TRUE)
save(plmTr,file="plmTr.RData")
firma <- FirmaModel(plmTr)
fit(firma, verbose=verbose)
fs <- getFirmaScores(firma)
-----------------------------------------------------------------------------------------------------------------------------
however, noticed that
1) None of the firma scores are negative. In the original paper, there were
many negative scores indicating exon skipping.
2) I also noticed that the firma scores are zeros for many probesets across
majority of the samples
3) For some columns, even though trFit is non-zero, I get all zero firma
scores
I am not sure what I am doign wrong. We are using the microarray expression
data (gene level data) from
http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE25219
Could someone help
Thanks
--
--
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/
---
You received this message because you are subscribed to the Google Groups
"aroma.affymetrix" group.
To unsubscribe from this group and stop receiving emails from it, send an email
to aroma-affymetrix+unsubscr...@googlegroups.com.
For more options, visit https://groups.google.com/d/optout.
