Hi,
I was trying to perform RMA on *Mouse Exon 1.0 ST Array* as described in
aroma website (link <http://www.aroma-project.org/replication/RMA>) using
custom cdf MoEx-1_0-st-v1,coreR1,A20080718,MR.cdf.gz
<http://www.aroma-project.org/data/annotationData/chipTypes/MoEx-1_0-st-v1/MoEx-1_0-st-v1,coreR1,A20080718,MR.cdf.gz>
.
I have executed following code in R
cdf <- AffymetrixCdfFile$byChipType(chipType, tags="coreR1,A20080718,MR")
cs <- AffymetrixCelSet$byName("data_CEL", cdf=cdf);
bc <- RmaBackgroundCorrection(cs);
csB <- process(bc);
qn <- QuantileNormalization(csB, typesToUpdate="pm");
csN <- process(qn);
plm <- RmaPlm(csN);
fit(plm);
ces <- getChipEffectSet(plm);
theta <- extractMatrix(ces);
rownames(theta) <- getUnitNames(cdf);
Error in `rownames<-`(`*tmp*`, value = c("6838637", "6992377", "6901592",
:
length of 'dimnames' [1] not equal to array extent
Please help me to understand this error and how can I solve this. The
session info is given below.
With regards
Rishi
R version 3.1.2 (2014-10-31)
Platform: x86_64-pc-linux-gnu (64-bit)
locale:
[1] LC_CTYPE=fi_FI.UTF-8 LC_NUMERIC=C
LC_TIME=en_GB LC_COLLATE=en_GB LC_MONETARY=fi_FI.UTF-8
[6] LC_MESSAGES=en_GB LC_PAPER=en_GB
LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_GB LC_IDENTIFICATION=C
attached base packages:
[1] stats4 parallel stats graphics grDevices utils datasets
methods base
other attached packages:
[1] preprocessCore_1.28.0 aroma.light_2.2.0
aroma.affymetrix_2.12.8 aroma.core_2.12.8
[5] R.devices_2.12.0 R.filesets_2.6.0
R.utils_1.34.0 R.oo_1.18.2
[9] R.methodsS3_1.6.2 affxparser_1.38.0
pd.moex10st.mm.aceviewg_0.0.1 affy_1.44.0
[13] BiocInstaller_1.16.1 pd.moex.1.0.st.v1_3.10.0
RSQLite_1.0.0 DBI_0.3.1
[17] moex10stmmrefseqcdf_19.0.0 AnnotationDbi_1.28.1
GenomeInfoDb_1.2.3 oligo_1.30.0
[21] Biostrings_2.34.0 XVector_0.6.0
IRanges_2.0.0 S4Vectors_0.4.0
[25] Biobase_2.26.0 oligoClasses_1.28.0
BiocGenerics_0.12.1
loaded via a namespace (and not attached):
[1] affyio_1.34.0 aroma.apd_0.5.0 base64enc_0.1-2
bit_1.1-12 codetools_0.2-8 digest_0.6.5
[7] DNAcopy_1.40.0 ff_2.2-13 foreach_1.4.2
GenomicRanges_1.18.3 iterators_1.0.7 matrixStats_0.12.2
[13] PSCBS_0.43.0 R.cache_0.11.0 R.huge_0.8.0
R.rsp_0.19.6 splines_3.1.2 tools_3.1.2
[19] zlibbioc_1.12.0
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