Hi,
you cannot use RMA on exon-arrays, you will need to use exon-aware
method such as FIRMA (e.g.
http://aroma-project.org/vignettes/FIRMA-HumanExonArrayAnalysis).
Hope this helps
Henrik
PS. For http://aroma-project.org/replication/RMA, I've updated it to
use `theta - extractTheta(ces)` instead of `theta -
extractMatrix(ces)`. This will allow you to set the row names. But
as you'll find out, 'theta' becomes an JxKxI array for exon-arrays,
where J is the number of genes, I is the number of samples and K is
the maximum number of exons per gene found. In other words, using
doRMA() on exon arrays gives you at best exon-specific estimates (and
they are not very good estimates - FIRMA is doing a much better job on
that).
On Wed, Dec 10, 2014 at 1:51 AM, Rishi Das Roy rishi.das...@gmail.com wrote:
Hi,
I was trying to perform RMA on Mouse Exon 1.0 ST Array as described in aroma
website (link) using custom cdf 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-8LC_NUMERIC=CLC_TIME=en_GB
LC_COLLATE=en_GBLC_MONETARY=fi_FI.UTF-8
[6] LC_MESSAGES=en_GB LC_PAPER=en_GB LC_NAME=C
LC_ADDRESS=CLC_TELEPHONE=C
[11] LC_MEASUREMENT=en_GBLC_IDENTIFICATION=C
attached base packages:
[1] stats4parallel 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_1.34.0R.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_19.0.0AnnotationDbi_1.28.1
GenomeInfoDb_1.2.3oligo_1.30.0
[21] Biostrings_2.34.0 XVector_0.6.0
IRanges_2.0.0 S4Vectors_0.4.0
[25] Biobase_2.26.0oligoClasses_1.28.0
BiocGenerics_0.12.1
loaded via a namespace (and not attached):
[1] affyio_1.34.0aroma.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_2.2-13foreach_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_3.1.2tools_3.1.2
[19] zlibbioc_1.12.0
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