Hello Aroma developers,
Attached session info and code. Platform windows.
I'm following steps
on http://www.aroma-project.org/vignettes/FIRMA-HumanExonArrayAnalysis/
In brief: I do background correct, normal quantile and perform ExonRmaPlm
I'm unable to decide and understand difference between ExonRmaPlm
and RmaPlm. Could the developers please shade light to when to use RmaPlm
in aroma?
Thanks.
--
--
When reporting problems on aroma.affymetrix, make sure 1) to run the latest
version of the package, 2) to report the output of sessionInfo() and
traceback(), and 3) to post a complete code example.
You received this message because you are subscribed to the Google Groups
"aroma.affymetrix" group with website http://www.aroma-project.org/.
To post to this group, send email to aroma-affymetrix@googlegroups.com
To unsubscribe and other options, go to http://www.aroma-project.org/forum/
---
You received this message because you are subscribed to the Google Groups
"aroma.affymetrix" group.
To unsubscribe from this group and stop receiving emails from it, send an email
to aroma-affymetrix+unsubscr...@googlegroups.com.
For more options, visit https://groups.google.com/d/optout.
R version 3.4.3 (2017-11-30)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows >= 8 x64 (build 9200)
Matrix products: default
locale:
[1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252
[3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C
[5] LC_TIME=English_United States.1252
attached base packages:
[1] stats4 parallel stats graphics grDevices utils datasets
methods base
other attached packages:
[1] aroma.light_3.8.0 aroma.affymetrix_3.1.0 aroma.core_3.1.1
R.devices_2.15.1
[5] R.filesets_2.12.1 R.utils_2.6.0 R.oo_1.21.0
affxparser_1.50.0
[9] R.methodsS3_1.7.1 limma_3.34.9 BiocInstaller_1.28.0
Cairo_1.5-9
[13] annotate_1.56.2 XML_3.98-1.10 AnnotationDbi_1.40.0
pd.huex.1.0.st.v2_3.14.1
[17] DBI_0.8 RSQLite_2.0 ff_2.2-13
bit_1.1-12
[21] oligo_1.42.0 Biostrings_2.46.0 XVector_0.18.0
IRanges_2.12.0
[25] S4Vectors_0.16.0 Biobase_2.38.0 oligoClasses_1.40.0
BiocGenerics_0.24.0
loaded via a namespace (and not attached):
[1] SummarizedExperiment_1.8.1 R.huge_0.9.0 DNAcopy_1.52.0
[4] listenv_0.7.0 splines_3.4.3 lattice_0.20-35
[7] base64enc_0.1-3 blob_1.1.1 bit64_0.9-7
[10] affyio_1.48.0 matrixStats_0.53.1
GenomeInfoDbData_1.0.0
[13] foreach_1.4.4 R.cache_0.13.0 zlibbioc_1.24.0
[16] future_1.8.0 codetools_0.2-15 memoise_1.1.0
[19] GenomeInfoDb_1.14.0 preprocessCore_1.40.0 Rcpp_0.12.16
[22] xtable_1.8-2 DelayedArray_0.4.1 PSCBS_0.63.0
[25] R.rsp_0.42.0 digest_0.6.15 GenomicRanges_1.30.3
[28] grid_3.4.3 tools_3.4.3 bitops_1.0-6
[31] RCurl_1.95-4.10 future.apply_0.1.0 pkgconfig_2.0.1
[34] Matrix_1.2-12 iterators_1.0.9 aroma.apd_0.6.0
[37] globals_0.11.0 compiler_3.4.3 cdf <- AffymetrixCdfFile$byChipType("HuEx-1_0-st-v2")
print(cdf)
cdf <- AffymetrixCdfFile$byChipType("HG-U133_Plus_2")
cs <- AffymetrixCelSet$byName("celfiles", cdf=cdf) # rawdata in cwd.
HuEx-1_0-st-v2 in celfiles # this should match cdf file names too
print(cs)
bc <- RmaBackgroundCorrection(cs) #backgroun
csBC <- process(bc,verbose=verbose)
qn <- QuantileNormalization(csBC, typesToUpdate="pm") #quantile norm
csN <- process(qn, verbose=verbose)
getCdf(csN) ##get CDF infor
plmTr <- ExonRmaPlm(csN, mergeGroups=TRUE) #entrire transcript #for
exon-by-exon mergeGroup make FALSE
print(plmTr)
