celsiusServer {celsius} | R Documentation |
Holds values like the URL needed to reach the server or the default timings for accessing the features and samples for the server etc.
new('celsiusServer',
celsiusUrl = ...., #URL
platform = ...., #Platform for data retrieval
protocol = ...., #Normalization protocol for the data to be
retrieved
stringency = ...., #Stringency setting for annotation retrieval
verbose = ...., #Verbosity preference
transform = ...., #Transform the annotations vector into 0's and
1's
retry = ...., #Number of retry attempts with web server
sampleTime = ...., #estimated time to retrieve a sample
featureTime = ...., #estimated time to retrieve a feature
)
celsiusUrl
"character"
to talk to a celsius server platform
"character"
for data retrieval. The preferred format is
the affymetrix format, but you can also enter Bioconductor
formatted platform names. Default is 'HG-U133A' protocol
"character"
for the data to be retrieved. Values can be:
'rma','vsn','gcrma','plier' and 'mas5'. Default value is 'rma'. stringency
"numeric"
. This is the quality of annotation desired. A
higher value results in more NA (un-annotated) values for
annotation retrieval. Possible values include:
600,500,400,300,200,100. Default is 500. verbose
"logical"
whether to print
output to the screen whenever data has been retrieved from the
DB. Default is FALSE. transform
"logical"
whether or not to
format all annotation mask data into a list of only 0's and 1's
(ie. to list NAs and and annotation conficts as 0's) Default is
FALSE. retry
"character"
for the client to attempt to get data from the
web server. Default is 3. sampleTime
"numeric"
to retrieve a sample from this platform (can
determine this by using time and the getSampleData() in this
library if you REALLY hate waiting) featureTime
"numeric"
to retrieve a feature from this platform (can
determine this by using time and the getFeatureData() in this
library if you REALLY hate waiting)Marc Carlson