R Analysis Options
Additional options for the analysis can be passed in the name string of the analysis. Below is a description of all recognized options.
The syntax for specifying an option is:
<analysis name> [<option name>=<option value> ....]
Spaces in an option must be escaped by a backslash.
Options can be strings or numbers. The string values "true", "false" or "null" and their uppercase counterparts are interpreted as booleans or the R NULL value.
File locations
dataRoot the root directory for the data filesconfig$dataRoot = "/srv/www/htdocs"
annoDir the directory where all chip annotation files are located
config$annoDir = "/opt/resolver/Rserve/annotations"
htmlDir the output html directory
config$htmlDir = "."
cssFile the CSS file to be included in the header of the report
config$cssFile = "/opt/resolver/Rserve/scripts/bfabStyle.css"
aptCommand the command to launch the Affymetrix Power Tools (APT)
config$aptCommand = "/opt/resolver/affymetrix/apt/Linux/bin/apt-probeset-summarize"
cdfRepository the directory with all the CDF files. The suffix .CDF of the files must be uppercase
config$cdfRepository = "/opt/resolver/Rserve/cdfRepository"
gseaDatabaseDir the directory with the geneset databases for the GSEA analysis
config$gseaDatabaseDir = "/opt/resolver/Rserve/annotations/GSEA/GeneSetDatabases"
logFile the file where the starting and the finishing of jobs is reported
config$logFile = "/opt/resolver/Rserve/jobLog.txt"
Probe Detection Thresholds
useSigThresh boolean flag telling whether a probe must have a signal above a threshold in order to be considered presentconfig$useSigThresh = TRUE
sigThresh the signal threshold for a probe to be present, only used if useSigThresh is TRUE. The Agilent QC method overwrits this threshold and sets it to 200.
config$sigThresh = 25
useDetectionPThresh boolean flag telling whether the detection p-value should be considered. Only used if the data has actually detection p-value, which is currenty only true for MAS5 processed Affy data.
config$useDetectionPThresh = FALSE
detectionPThresh threshold for the detection p-value, see useDetectionPThresh
config$detectionPThresh = 0.05
Input and Preprocessing Options
AgilentSignalColumn the column to read from Agilent TXT files. For two channel data the corresponding control signal column is a also read. Common choices are "gMedianSignal", "gProcessedSignal", "LogRatio". For "LogRatio" the control columnb will be "gProcessedSignal"config$AgilentSignalColumn = "gMedianSignal"
AgilentFlagColumn the column in the Agilent File that provides the present flags
config$AgilentFlagColumn = "gIsWellAboveBG"
loadAgilentFeatureData for Agilent files the loaded signal always holds one value per probe. Replicate spots/features are averaged. If this is true, the original feature values are also kept and stored in the rawData as featureSignal.
config$loadAgilentFeatureData = FALSE
useBarcodeAsReplicateId this will load the slide barcode and fill the replicate slot of the sample annotation with the barcode. Using this flag is deprecated.
config$useBarcodeAsReplicateId = FALSE
normMethod Normalization method to be used. Valid options are: "none", "quantile", "logMean", "vsn". Different analyses will use different default normalizations. The normalization used is reported in the HTML-Report.
config$normMethod = "quantile"
doBatchNorm whether batch normalization usign the pamr package should be applied. As a side effect this normalizes each probe to mean 1, which means that signal thresholding can not be used in combination with this flag. Requires in the sample annotation a column called "batch" that indicates the batch for each sample.
config$doBatchNorm = FALSE
AffyPreprocessing preprocessing method for Affy data, supported values are "rma" and "mas5"
config$AffyPreprocessing = "rma"
runMas5 flag whether additionally MAS5 processing should be run
config$runMas5 = FALSE
useFirstExonOnly flag whether for exon arrays only probe sets in the 5'-exon of genes should be used. Only for exploratory analysis checking for degradation
config$useFirstExonOnly = FALSE
useLastExonOnly flag whether for exon arrays only probe sets in the 3'-exon of genes should be used. Only for exploratory analysis checking for degradation.
config$useLastExonOnly = FALSE
useExonicOnly should only "exon"-targeting probe sets as defined by the xmap annotation database be used?. Only relevant when using exon arrays. Speeds up processing and reduces false positives when only looking for expression in well defined genes.
config$useExonicOnly = FALSE
removePoorAffyProbes should probes that have a signal above affyPorbeSignalFilterThresh in less than minAffyPresentProbeValues samples be removed?. Particularly useful for tiling arrays where many probes may have bad hybridization properties
config$removePoorAffyProbes = FALSE
affyProbeSignalFilterThresh threshold for removal of "non-working" probes on Affy chips
config$affyProbeSignalFilterThresh = 32
minAffyPresentProbeValues number of samples in which a value above affyProbeSignalFilterThresh is required in order to keep a probe
config$minAffyPresentProbeValues = 3
minAffyProbeCount min number of probes to keep in a probe set, even if some of them are "non-working"
config$minAffyProbeCount = 3
exonLevelCdf set of cdfs that define exon-level probe sets and for which exon-level analyses can be applied
config$exonLevelCdf = c("ratexonpm", "mouseexonpm", "exon.pm", "ratexonprobeset")
xmapCdf set of cdfs that are available in the xmap database
config$xmapCdf = c("ratexonpm", "mouseexonpm", "exon.pm")
Plotting Options
writeScatterPlots flag telling whether scatter plots should be drawnconfig$writeScatterPlots = TRUE
- logColorRange
- topGeneSize
- maxGenesForClustering
- minGenesForClustering
- showGeneClusterLabels
- plotDegradation
- highVarThreshold
Differential Expression Options
- minimalLog2Effect
- pValueHighlightThresh
- log2RatioHighlightThresh
- testMethod
- tukeyThresh
Gene Set Analysis Options
- runGO
- runMetaCore
- pValThreshGO
- log2RatioThreshGO
- pValThreshFisher
- pValThreshFisherKegg
- minCountFisher
- runGSEA
- pValThreshGsea
- maxNumberGroupsDisplayed — the maximum number of GO groups to show in the tables, default: 40
Output Options
- writeAllProbes
- doZip
- writeAffyTxt
Annotation Options
- probeAnnotationFromBioC
- geneColumnSet
- useAnnotationFromFile
Other Options
- printChips — print some header information from the loaded Agilent files on stdout, default: false
- saveImage — save an image at the end of the analysis, default: false
- saveRawData — save an .RData file holding the rawData Object right after import, default: false
- subsetProbes