Dear All,
I am analyzing human affy exon arrays for first time. I followed the
steps listed in website:
http://groups.google.com/group/aroma-affymetrix/web/human-exon-array-analysis
In summarization step, I met an error when I began to fit the PLM to
all of the data.
Thanks
Hailei
my R session:
> sessionInfo()
R version 2.10.0 Under development (unstable) (2009-08-10 r49148)
x86_64-unknown-linux-gnu
My script:
library(aroma.affymetrix)
verbose <- Arguments$getVerbose(-8,timestamp=TRUE)
chipType <- "HuEx-1_0-st-v2"
cdf <- AffymetrixCdfFile$byChipType(chipType,
tags="coreR3,A20071112,EP")
print(cdf)
cs <- AffymetrixCelSet$byName("tissues",cdf=cdf)
print(cs)
bc <- RmaBackgroundCorrection(cs, tag="coreR3")
csBC <- process(bc,verbose=verbose)
qn <- QuantileNormalization(csBC, typesToUpdate="pm")
print(qn)
csN <- process(qn, verbose=verbose)
plmTr <- ExonRmaPlm(csN, mergeGroups=TRUE)
print(plmTr)
fit(plmTr,verbose=verbose)
The error is:
> fit(plmTr, verbose=verbose)
20091015 15:49:54|Fitting model of class ExonRmaPlm:...
ExonRmaPlm:
Data set: tissues
Chip type: HuEx-1_0-st-v2,coreR3,A20071112,EP
Input tags: coreR3,QN
Output tags: coreR3,QN,RMA,merged
Parameters: (probeModel: chr "pm"; shift: num 0; flavor: chr
"affyPLM"; treatNAsAs: chr "weights"; mergeGroups: logi TRUE).
Path: plmData/tissues,coreR3,QN,RMA,merged/HuEx-1_0-st-v2
RAM: 0.01MB
20091015 15:49:54| Identifying non-estimated units...
20091015 15:49:54| Identifying non-fitted units in chip-effect
file...
20091015 15:49:54| Pathname: plmData/tissues,coreR3,QN,RMA,merged/
HuEx-1_0-st-v2/RD2009092837,chipEffects.CEL
20091015 15:49:54| Found indices cached on file
20091015 15:49:54| Reading data for these 18708 cells...
20091015 15:49:54| Reading data for these 18708 cells...done
20091015 15:49:54| Looking for stdvs <= 0 indicating non-estimated
units:
int [1:18708] 1 2 3 4 5 6 7 8 9 10 ...
20091015 15:49:54| Identifying non-fitted units in chip-effect
file...done
20091015 15:49:54| Identifying non-estimated units...done
20091015 15:49:54| Getting model fit for 18708 units.
<simpleError in .Call("R_rlm_rma_default_model", y, psiCode, psiK,
PACKAGE = rlmPkg): Incorrect number of arguments (3), expecting 4 for
R_rlm_rma_default_model>
Error in list(`fit(plmTr, verbose = verbose)` = <environment>,
`fit.ProbeLevelModel(plmTr, verbose = verbose)` = <environment>, :
[2009-10-15 15:49:54] Exception: The fit function for requested exon
RMA PLM failed
at throw(Exception(...))
at throw.default("The fit function for requested exon RMA PLM
failed")
at throw("The fit function for requested exon RMA PLM failed")
at getFitUnitGroupFunction.ExonRmaPlm(this, ...)
at getFitUnitGroupFunction(this, ...)
at getFitUnitFunction.MultiArrayUnitModel(this)
at getFitUnitFunction(this)
at fit.ProbeLevelModel(plmTr, verbose = verbose)
at fit(plmTr, verbose = verbose)
20091015 15:49:54|Fitting model of class ExonRmaPlm:...done
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