loadMAdata(datadir = getwd(), setup = "setup.txt", dataNorm, platform = "NULL", annotation, normalization = "plier", filter = TRUE, verbose = TRUE, ...)
getwd()
.
data.frame
or similar containing the experimental
setup. Defaults to "setup.txt"
, see details below for more information.
data.frame
or similar containing the normalized data. Only to be used if
the user wishes to start with normalized data rather then CEL files.
"yeast2"
or NULL
. See details below for more information.
data.frame
or similar containing the annotation information. The annotation
should consist of the columns Gene name, Chromosome and
Chromosome location. Not required if platform="yeast2"
.
"plier"
,
"rma"
or "mas5"
. Defaults to "plier"
.
TRUE
then probes not present in the
annotation will be discarded. Defaults to TRUE
.
TRUE
.
ReadAffy
.
ArrayData
object (which is essentially a list
) with the
following elements:data.frame
containing normalized expression valuesdata.frame
containing experimental setupdata.frame
containing annotationArrayData
object may not include
dataRaw
and/or annotation
.datadir
or normalized data specified by dataNorm
,
and (2) experimental setup specified by setup
. The setup shold be either a tab delimited text file with column headers or a
data.frame
. The first column should contain the names of the CEL files
or the column names used for the normalized data, please be sure to use names valid as
column names, e.g. avoid names starting with numbers. Additional columns should
assign attributes in some category to each array. (For an example run the example
below and look at the object myArrayData$setup
.)
The piano package is customized for yeast 2.0 arrays and annotation will
work automatically, if the cdfName of the arrays equals Yeast_2. If using
normalized yeast 2.0 data as input, the user needs to set the argument
platform="yeast2"
to tell the function to use yeast annotation. If other
platforms than yeast 2.0 is used, set platform=NULL
(default) and supply
appropriate annotation by the argument annotation
. Note that the cdfName
will override platform
, so it can still be set to NULL
for yeast
2.0 CEL files. Note also that annotation
overrides platform
, so
if the user wants to use an alternative annotation for yeast, this can be done
simply by specifying this in annotation
.
The annotation should have the column headers Gene name, Chromosome and
Chromosome location. The Gene name is used in the heatmap in
diffExp
and the Chromosome and Chromosome location is used
by the polarPlot
. The rownames (or first column if using a text file)
should contain the probe IDs. If using a text file the first column should
have the header probeID or similar. The filtering step discards all probes
not listed in the annotation.
Normalization is performed on all CEL file data using one of the Affymetrix methods:
PLIER ("plier"
) as implemented by justPlier
,
RMA (Robust Multi-Array Average) ("rma"
) expression measure as implemented
by rma
or
MAS 5.0 expression measure "mas5"
as implemented by mas5
.
It is possible to pass additional arguments to ReadAffy
, e.g.
cdfname
as this might be required for some types of CEL files.
runQC
, diffExp
,
ReadAffy
, expresso
, justPlier
,
yeast2.db
# Get path to example data and setup files:
dataPath <- system.file("extdata", package="piano")
# Load normalized data:
myArrayData <- loadMAdata(datadir=dataPath, dataNorm="norm_data.txt.gz", platform="yeast2")
# Print to look at details:
myArrayData
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