[BioC] support for miRNA-1_0?

[cstrato]

Dear Dick,

Some weeks ago I have updated package xps to allow some support of the 
miRNA aray, and have uploaded "xps_1.5.13" to the BioC development branch.

Here is the code to create the scheme and import the CEL-files:

# import scheme:
# note: you need to rename "miRNA-1_0.probe_list.20081203.txt" to 
"miRNA-1_0.probe.tab"
libdir <- "/Volumes/GigaDrive/Affy/libraryfiles"
scmdir <- "/Volumes/GigaDrive/CRAN/Workspaces/Schemes"
scheme.mirna <- import.expr.scheme("Scheme_miRNA_1_0",filedir=scmdir,
                paste(libdir,"miRNA-1_0.CDF",sep="/"),
                paste(libdir,"miRNA-1_0.probe.tab",sep="/"))

# import CEL-files (test files from Affymetrix)
datdir <- getwd()
celdir <- "/Volumes/GigaDrive/ChipData/miRNA/genisphere_affymetrix_dataset"
celnames <- c("BrainTotal", "LiverLMW", "LiverTotal")
data.mirna <- 
import.data(scheme.mirna,"DatamiRNA",filedir=datdir,celdir=celdir,celnames=celnames)

As you see, you need to rename the probe file and you cannot use the 
special Affymetrix annotation file since it does not follow the standard 
annotation layout.


In a new R session you can load the scheme and data files as usual, and 
do RMA:

# load scheme and data
scmdir <- "/Volumes/GigaDrive/CRAN/Workspaces/Schemes"
datdir <- getwd()
scheme.mirna <- root.scheme(paste(scmdir,"Scheme_miRNA_1_0.root",sep="/"))
data.mirna <- root.data(scheme.mirna, 
paste(datdir,"DatamiRNA_cel.root",sep="/"))

# RMA
data.rma <- 
rma(data.mirna,"miRNA_RMA",tmpdir="",background="pmonly",normalize=T)

# get expression level data.frames
expr.rma <- validData(data.rma)
head(expr.rma)


You can also do some visualization:

# for raw data you need to attach data first
data.mirna <- attachMask(data.mirna)
data.mirna <- attachInten(data.mirna)

# plots
image(data.mirna)
hist(data.mirna)
boxplot(data.mirna)
hist(data.rma)
boxplot(data.rma)

Please note that currently all probesets for all different organisms are 
used for RMA.

Since I have no access to miRNA data, I would be interested in reports 
from users trying xps for miRNA, especially if RMA normalization gives 
reasonable results.

Best regards
Christian
_._._._._._._._._._._._._._._._._._
C.h.r.i.s.t.i.a.n   S.t.r.a.t.o.w.a
V.i.e.n.n.a           A.u.s.t.r.i.a
e.m.a.i.l:        cstrato at aon.at
_._._._._._._._._._._._._._._._._._


Dick Beyer wrote:
> Are there any plans to support the new affy microRNA chip: miRNA-1_0?
>
> Thanks,
> Dick
>
> ******************************************************************************* 
>
> Richard P. Beyer, Ph.D.    University of Washington
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