search for: genepixdata

Hi. Is it possible to make gpr from raw? library(aroma) #read gpr file gpr <- GenePixData$read("gpr123.gpr", path=aroma$dataPath) # gpr -> raw raw <- as.RawData(gpr) # raw -> ma ma <- getSignal(raw, bgSubtract=FALSE) ma.norm <- clone(ma) #normalization normalizeWithinSlide(ma.norm, "s") #ma -> raw raw2 <- as.RawData(ma) I want to make gpr data...

...re hard to reproduce and took time to find. It would be nice if the [R] parser, or some previous engine that reads the source file, could given an explicit error saying that the "line was too long". EXAMPLE: In my case I got in perl '@Rfiles' was: "R/LogBook.R R/LogEntry.R R/GenePixData.R R/Layout.R R/ImaGeneData.R R/MicroarrayData.PLOT.R R/QualityData.R R/MicroarrayData.R R/MAData.R R/MAData.NORM.R R/zzz.R R/Replicates.R R/SMA.R R/FieldFilter.R R/Filter.R R/QuantArrayData.R R/RGData.R R/RawData.R R/000.R R/MicroarrayData.IO.R R/LayoutGroups.R R/BFilter.R R/com.braju.sma.R R/Copy...

...ome previous engine that reads > > the source file, > > > could given an explicit error saying that the "line was too long". > > > > > > EXAMPLE: > > > In my case I got in perl '@Rfiles' was: > > > "R/LogBook.R R/LogEntry.R R/GenePixData.R R/Layout.R R/ImaGeneData.R > > > R/MicroarrayData.PLOT.R R/QualityData.R R/MicroarrayData.R R/MAData.R > > > R/MAData.NORM.R R/zzz.R R/Replicates.R R/SMA.R R/FieldFilter.R > > R/Filter.R > > > R/QuantArrayData.R R/RGData.R R/RawData.R R/000.R R/MicroarrayData.IO.R...

...e nice if the [R] parser, or some previous engine that reads > the source file, > > could given an explicit error saying that the "line was too long". > > > > EXAMPLE: > > In my case I got in perl '@Rfiles' was: > > "R/LogBook.R R/LogEntry.R R/GenePixData.R R/Layout.R R/ImaGeneData.R > > R/MicroarrayData.PLOT.R R/QualityData.R R/MicroarrayData.R R/MAData.R > > R/MAData.NORM.R R/zzz.R R/Replicates.R R/SMA.R R/FieldFilter.R > R/Filter.R > > R/QuantArrayData.R R/RGData.R R/RawData.R R/000.R R/MicroarrayData.IO.R > > R/LayoutG...

...> part. > > > Input files are in the following order: > > oligo.prest.out for parse.RData to work. Produces the next input file > > oligolista for Korrelation.RData to work, which also needs the input file > > 8_SkBr _13433630.gpr. > > > The function GenePixData can be found in the aroma package. > > Thank you for your help, 1. Package kth is unavailable for us. 2. I do not know anything about a package called "aroma", it is neither on CRAN nor in the BioC repositories. 3. Can you please also try to make your example smaller? 4. The...