Hi,
I have two datasets from HTA platform for which I want to do fRMA normalisation(specifically). As I understand fRMA works with either affybatch object(package affy) or ExpressionFeatureSet(package oligo). How can I do this by using custom cdf file from brain array resource? I have tried using the "hta20hsensgprobe" package from brainarray website and used the following lines of code:
library(oligo) library(hta20hsensgprobe) celFiles<- list.celfiles( "HTA_data",full.names = TRUE) affyRaw <- read.celfiles(celFiles,pkgname="hta20hsensgprobe")
But this gives me the following error:
Error in (function (classes, fdef, mtable) : unable to find an inherited method for function ‘kind’ for signature ‘"probetable"’
The sessionInfo is as follows:
R version 3.1.2 (2014-10-31) Platform: x86_64-apple-darwin10.8.0 (64-bit) locale: [1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8 attached base packages: [1] stats4 parallel stats graphics grDevices utils datasets methods base other attached packages: [1] hta20hsensgprobe_19.0.0 AnnotationDbi_1.28.2 GenomeInfoDb_1.2.4 pd.hta.2.0_3.10.1 RSQLite_1.0.0 DBI_0.3.1 [7] Biostrings_2.34.1 XVector_0.6.0 IRanges_2.0.1 S4Vectors_0.4.0 oligoClasses_1.28.0 frma_1.18.0 [13] Biobase_2.26.0 BiocGenerics_0.12.1 data.table_1.9.4 aroma.light_2.2.1 aroma.affymetrix_2.13.1 aroma.core_2.13.0 [19] R.devices_2.13.0 R.filesets_2.7.1 R.utils_2.0.2 R.oo_1.19.0 oligo_1.30.0 affxparser_1.38.0 [25] R.methodsS3_1.7.0 loaded via a namespace (and not attached): [1] affy_1.44.0 affyio_1.34.0 aroma.apd_0.6.0 base64enc_0.1-3 BiocInstaller_1.16.2 bit_1.1-12 Cairo_1.5-5 [8] chron_2.3-45 codetools_0.2-11 digest_0.6.8 DNAcopy_1.40.0 ff_2.2-13 foreach_1.4.2 GenomicRanges_1.18.4 [15] iterators_1.0.7 magrittr_1.5 MASS_7.3-39 matrixStats_0.14.0 plyr_1.8.2 preprocessCore_1.28.0 PSCBS_0.44.0 [22] R.cache_0.11.0 R.huge_0.9.0 R.rsp_0.20.0 Rcpp_0.11.6 reshape2_1.4.1 splines_3.1.2 stringi_0.4-1 [29] stringr_1.0.0 tools_3.1.2 zlibbioc_1.12.0
Thanks in advance.
Regards,
Sanjana

