subtractBackground |
logical |
spotsRemovedBeforeNormalisation |
vector of character strings;
all spots which match the strings are removed from
the the whole analysis, i.e. already before normalisation |
spotsSetToZeroWeightAndRemovedAfterNormalisation |
vector of character strings;
all spots which match the strings become zero weight
(weights are only used by loess type normalisations) and
are removed after normalisation |
spotIdentifier |
character string |
mergeSlides |
logical; at this point only used for consistency tests
of a hypothetical slide merge operation with respect to mergeSlidesColumn |
slideDescriptionFile |
character string;
the first line of the file must contain all column names,
in particular the column fileNameColum and possibly
slideNumberColumn
must be included |
fileNameColumn |
character string; required; default: "fileName" |
slideNumberColumn |
character string; optional; if missing it is set
to fileNameColumn ; default: missing |
mergeSlidesColumn |
character string; optional;
cf. mergeSlides |
sampleAnnotationColumns |
possible values:
a vector of character strings or NA ;
sampleAnnotationColumns define
all columns (hybridisation covariates)
which are relevant for any further analysis.
If mergeSlides is set to TRUE
the annotation should be consistent for replicas.
All columns in slideDescriptionFile are taken
if set to NULL and all except of
fileNameColumn and slideNumberColumn are taken
if set to NA . |
loadPath |
character string;
the path is used to load the slideDescriptionFile and data files;
note: . refers to the current/working directory
|
savePath |
character string;
the path is used to save the results
if the path does not exist a directory is created;
note: . refers to the current/working directory
|
normalisationMethod |
character string; default: "vsn"; cf.
normalise |
imageFileType |
character string; default: "GenePix"; cf.
readImageFiles |
channelsSeparately |
logical; default FALSE |
hybridisationGroups |
list of numeric vectors; default missing |
objectsFileName |
character string; filename for saving of list of result objects |
plotOutput |
character string specifying
either "screen" or "pdf"; default: "screen" |