Dear group,
I would like to extract a data.frame on the exon level and followed
these commands (see below), surprisingly the data.frame had these
dimensions:
326983 249
while I expected to have a data.frame with
1.4 Mill 249 samples
Could you please advise me how I can extract the data for all exons
from this analysis?
Many thanks for your advise in advance,
best wishes,
Anita
library(aroma.affymetrix)
library(Biobase)
library(limma)
library(affy)
library(biomaRt)
##############################################################################
verbose <- Arguments$getVerbose(-8, timestamp=TRUE)
chipType <- "HuEx-1_0-st-v2"
cdf <- AffymetrixCdfFile$byChipType(chipType,tags="U-Ensembl49,G-
Affy")
print(cdf)
cs <- AffymetrixCelSet$byName("Affy_Exon_June2011", cdf=cdf)
print(cs)
setCdf(cs,cdf)
bc <- RmaBackgroundCorrection(cs,tag="U-Ensembl49,G-Affy")
csBC <- process(bc,verbose=verbose)
qn <- QuantileNormalization(csBC,typesToUpdate="pm")
print(qn)
csN <- process(qn,verbose=verbose)
getCdf(csN)
plmEx <- ExonRmaPlm(csN,mergeGroups=FALSE)
print(plmEx)
fit(plmEx,verbose=verbose)
cesEx <- getChipEffectSet(plmEx)
exFit <- extractDataFrame(cesEx,units=NULL,addNames=TRUE)
dim(exFit)
#326983 - 249 - exon based data
##############################################################################
sessionInfo()
R version 2.12.1 (2010-12-16)
Platform: x86_64-unknown-linux-gnu (64-bit)
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] biomaRt_2.6.0 aroma.affymetrix_2.1.0 aroma.apd_0.1.8
[4] affxparser_1.22.1 R.huge_0.2.2 aroma.core_2.1.0
[7] aroma.light_1.20.0 matrixStats_0.2.2 R.rsp_0.5.3
[10] R.cache_0.4.2 R.filesets_1.0.1 digest_0.5.0
[13] R.utils_1.7.5 R.oo_1.8.0 affy_1.28.1
[16] R.methodsS3_1.2.1 limma_3.6.9 Biobase_2.10.0
loaded via a namespace (and not attached):
[1] affyio_1.18.0 preprocessCore_1.12.0 RCurl_1.6-6
[4] tcltk_2.12.1 tools_2.12.1 XML_3.4-0
>
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