Question: Using custom CDF with 'make.cdf.env'
5.2 years ago by
Guest User • 12k
Guest User • 12k wrote:
Dear List, I made a custom CDF by modifying the original Affymetrix miRNA v1 file. As there is a great level of redundancy in this chip I have condensed the original 7815 probe sets into 6190 probe sets (by 'moving' probes from one set to another), however when I try making and attaching my new CDF environment I still seem to have 7815 probe sets so presumably I must have done something wrong. I have read the vignette and many similar posts to mine however still cannot work out what I am doing wrong. Perhaps the problem is with the CDF itself? I have a short script testing the functionality, the output of which I have copied in below. I will gladly attach the script, CDFs and example CEL file if there is nothing obviously wrong with the code - would do this now but there doesn't appear to be an option on the webform. Many thanks, Scott > folder <- "C:\Work\COPD-ASTHMA\microRNA files\newCDF\test\" > > setwd(paste0(folder,"CEL")) > options(stringsAsFactors=FALSE) > library(affy) Loading required package: BiocGenerics Loading required package: parallel Attaching package: ???BiocGenerics??? The following objects are masked from ???package:parallel???: clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, clusterMap, parApply, parCapply, parLapply, parLapplyLB, parRapply, parSapply, parSapplyLB The following object is masked from ???package:stats???: xtabs The following objects are masked from ???package:base???: anyDuplicated, as.data.frame, cbind, colnames, duplicated, eval, Filter, Find, get, intersect, lapply, Map, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank, rbind, Reduce, rep.int, rownames, sapply, setdiff, sort, table, tapply, union, unique, unlist Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. > library(makecdfenv) Loading required package: affyio > > cleancdfname("newmir1.cdf")  "newmir1.cdf" > newmir1 = make.cdf.env("newmir1.cdf") Reading CDF file. Creating CDF environment Wait for about 78 dots................................................ ....................... > Data <- ReadAffy() > Data at cdfName <- "newmir1" > > Data AffyBatch object size of arrays=230x230 features (17 kb) cdf=newmir1 (7815 affyids) number of samples=1 number of genes=7815 annotation=mirna102xgain notes= > > dim(exprs(rma(Data))) Background correcting Normalizing Calculating Expression  7815 1 -- output of sessionInfo(): > sessionInfo() R version 3.0.2 (2013-09-25) Platform: x86_64-w64-mingw32/x64 (64-bit) locale:  LC_COLLATE=English_United Kingdom.1252  LC_CTYPE=English_United Kingdom.1252  LC_MONETARY=English_United Kingdom.1252  LC_NUMERIC=C  LC_TIME=English_United Kingdom.1252 attached base packages:  parallel stats graphics grDevices utils datasets methods  base other attached packages:  makecdfenv_1.36.0 affyio_1.28.0 affy_1.38.1 Biobase_2.20.1  BiocGenerics_0.6.0 loaded via a namespace (and not attached):  BiocInstaller_1.10.4 preprocessCore_1.22.0 tools_3.0.2  zlibbioc_1.6.0 -- Sent via the guest posting facility at bioconductor.org.
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