[BioC] Using custom CDF with 'make.cdf.env'

[Scott Robinson]

Dear All,

Since it exceeds 1MB, here is a link to the old ("miRNA-1_0.CDF") and new ("newmir1.cdf") CDFs, test script and example CEL file:

http://www.files.com/set/53fdeb0aa2176

Thanks,

Scott
________________________________________
From: Scott Robinson [guest] [guest at bioconductor.org]
Sent: 27 August 2014 13:11
To: bioconductor at r-project.org; Scott Robinson
Cc: makecdfenv Maintainer
Subject: Using custom CDF with 'make.cdf.env'

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")
[1] "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
[1] 7815    1


 -- output of sessionInfo():

> sessionInfo()
R version 3.0.2 (2013-09-25)
Platform: x86_64-w64-mingw32/x64 (64-bit)

locale:
[1] LC_COLLATE=English_United Kingdom.1252
[2] LC_CTYPE=English_United Kingdom.1252
[3] LC_MONETARY=English_United Kingdom.1252
[4] LC_NUMERIC=C
[5] LC_TIME=English_United Kingdom.1252

attached base packages:
[1] parallel  stats     graphics  grDevices utils     datasets  methods
[8] base

other attached packages:
[1] makecdfenv_1.36.0  affyio_1.28.0      affy_1.38.1        Biobase_2.20.1
[5] BiocGenerics_0.6.0

loaded via a namespace (and not attached):
[1] BiocInstaller_1.10.4  preprocessCore_1.22.0 tools_3.0.2
[4] zlibbioc_1.6.0

--
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