[BioC] Using custom CDF with 'make.cdf.env'
Scott Robinson [guest]
guest at bioconductor.org
Wed Aug 27 14:11:29 CEST 2014
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.
> folder <- "C:\Work\COPD-ASTHMA\microRNA files\newCDF\test\"
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: âBiocGenericsâ
The following objects are masked from âpackage:parallelâ:
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following object is masked from âpackage:statsâ:
The following objects are masked from âpackage:baseâ:
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")'.
Loading required package: affyio
> newmir1 = make.cdf.env("newmir1.cdf")
Reading CDF file.
Creating CDF environment
Wait for about 78 dots.......................................................................
> Data <- ReadAffy()
> Data at cdfName <- "newmir1"
size of arrays=230x230 features (17 kb)
cdf=newmir1 (7815 affyids)
number of samples=1
number of genes=7815
 7815 1
-- output of sessionInfo():
R version 3.0.2 (2013-09-25)
Platform: x86_64-w64-mingw32/x64 (64-bit)
 LC_COLLATE=English_United Kingdom.1252
 LC_CTYPE=English_United Kingdom.1252
 LC_MONETARY=English_United Kingdom.1252
 LC_TIME=English_United Kingdom.1252
attached base packages:
 parallel stats graphics grDevices utils datasets methods
other attached packages:
 makecdfenv_1.36.0 affyio_1.28.0 affy_1.38.1 Biobase_2.20.1
loaded via a namespace (and not attached):
 BiocInstaller_1.10.4 preprocessCore_1.22.0 tools_3.0.2
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