Hi Enid.
I was unsuccessful in repeating your problem. I ran the script below
from a fresh session on the Affy tissues dataset using
aroma.affymetrix 1.2.0 ... and I get results. I don't think I've run
FIRMA on as few as 4 samples as your example suggests, but in theory
that shouldn't be the problem.
Can you post your full script and give your sessionInfo()?
Cheers,
Mark
-----------
library(aroma.affymetrix)
# setup
verbose <- Arguments$getVerbose(-20, timestamp=TRUE)
chipType <- "HuEx-1_0-st-v2"
cdf <- AffymetrixCdfFile$byChipType(chipType,
tags="coreR3,A20071112,EP")
cs <- AffymetrixCelSet$byName("tissues", cdf=cdf)
# BG adjust + QN
bc <- RmaBackgroundCorrection(cs, tag="coreR2")
csBC <- process(bc,verbose=verbose)
qn <- QuantileNormalization(csBC, typesToUpdate="pm")
csN <- process(qn, verbose=verbose)
# fit PLM, FIRMA
plm <- ExonRmaPlm(csN, mergeGroups=TRUE)
rs <- calculateResiduals(plm, verbose=verbose)
firma <- FirmaModel(plm)
fit(firma, verbose=verbose)
fs <- getFirmaScores(firma)
firmascore <- extractDataFrame(fs)
-----------
On 5-Oct-09, at 7:50 AM, Enid wrote:
>
> Dear all,
>
> I am analysing a set of exon array data, and have been following the
> human exon array analysis vignette, but am having trouble getting the
> firma scores
>
> After the firma analysis, I get a table full of NaN's.
>
>> firma <- FirmaModel(plmTr)
>> fit(firma, verbose=verbose)
>> fs <- getFirmaScores(firma)
>> firmascore<-extractDataFrame(fs)
>> firmascore[1:10,]
> unit group cell P2008 P2009 P2010 P2011
> 1 1 1 1 NaN NaN NaN NaN
> 2 1 2 2 NaN NaN NaN NaN
> 3 2 1 3 NaN NaN NaN NaN
> 4 2 2 4 NaN NaN NaN NaN
> 5 2 3 5 NaN NaN NaN NaN
> 6 2 4 6 NaN NaN NaN NaN
> 7 3 1 7 NaN NaN NaN NaN
> 8 3 2 8 NaN NaN NaN NaN
> 9 3 3 9 NaN NaN NaN NaN
> 10 3 4 10 NaN NaN NaN NaN
>
> but the transcript summarisation seems to be ok.
>
>> readUnits(plmTr,unit=1)
> $`2315251`
> $`2315251`[[1]]
> $`2315251`[[1]]$intensities
> [,1] [,2] [,3] [,4]
> [1,] 6.418280 51.159870 5.914537 8.396150
> [2,] 11.297100 7.589603 11.975643 8.396150
> [3,] 9.184888 12.899874 83.409866 44.409882
> [4,] 8.778770 5.476091 82.909866 5.136143
> [5,] 4.446828 6.080955 11.454535 4.062980
> [6,] 5.914537 4.550271 7.589603 3.849267
> [7,] 8.038540 3.542727 3.808023 7.923751
> [8,] 13.260725 6.238900 4.660217 4.200828
>
> I have not sure what I'm doing wrong and would really appreciate any
> help.
>
> Thank you very much in advance,
> Enid
>
> >
------------------------------
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
------------------------------
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