Last chance! 50% off unlimited learning
Sale ends in
makeGEOSubmissionFiles(normData, rawData, forceDetection = TRUE, basename = "GEO", softTemplate = NULL)
createGEOMeta(normData,basename)
createGEOMatrix(normData,forceDetection=TRUE,basename="GEO",softTemplate=NULL,normalised=T)
Meta file: A template file that can be used to record all the relevant metadata for the experiment, plus the information required by GEO. The SAMPLES section of the file contains the per-sample metadata and has columns generate from the required GEO data an the phenoData stored with the input data\
Processed Matrix - GEO seems to want normalised intensities and detection scores for each probe on each array. Detection scores can be generated if they are not present in the data. The probes that are reported in this file are decided using the annotation slot of the object and querying the appropriate annotation package. Otherwise, a SOFT file downloaded from GEO can be used. \ Raw Matrix - As above, but non-normalised intensities are used
## Not run:
# if(require(beadarrayExampleData)){
# data(exampleSummaryData)
# rawdata <- channel(exampleSummaryData, "G")
# normdata <- normaliseIllumina(rawdata)
# makeGEOSubmissionFiles(normdata, rawdata)
#
#
# ##To annotate against a SOFT file that can be downloaded from GEO
# ##e.g. ftp://ftp.ncbi.nlm.nih.gov/geo/platforms/GPL10nnn/GPL10558/annot/GPL10558.annot.gz
#
# makeGEOSubmissionFiles(normdata, rawdata,softTemplate="GPL10558.annot")
# }
#
# ## End(Not run)
Run the code above in your browser using DataLab