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

[James W. MacDonald]

Hi Scott,

As far as I can tell, you haven't made any changes to the cdf at all:

> z <- make.cdf.env("newmir1.cdf")
Reading CDF file.
Creating CDF environment
Wait for about 78
dots.........................................................................
> z
<environment: 0x00000000113d5c08>
> length(ls(z))
[1] 7815
> zz <- as.list(z)
> table(sapply(zz, nrow))

   4    8    9   10   11   20   25   40   50   67   73   88   89   90   91
  92   94
6703    8   14   32  959    9    1    1    2    1    1    1    2    1    1
   1   78
> y <- make.cdf.env("miRNA-1_0.CDF")
Reading CDF file.
Creating CDF environment
Wait for about 78
dots..........................................................................
> yy <- as.list(y)
> length(yy)
[1] 7815
> table(sapply(yy, nrow))

   4    8    9   10   11   20   25   40   50   67   73   88   89   90   91
  92   94
6703    8   14   32  959    9    1    1    2    1    1    1    2    1    1
   1   78
> all.equal(names(zz), names(yy))
[1] TRUE

Best,

Jim




On Wed, Aug 27, 2014 at 10:31 AM, Scott Robinson <
Scott.Robinson at glasgow.ac.uk> wrote:

> 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
>
> --
> Sent via the guest posting facility at bioconductor.org.
>



-- 
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099

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