March 25 2004 README addition from VJ Carey: This is an R package for access to Wolfgang’s contributed kidney data. I have just used save(compress=TRUE) for some of the data, and added some trivial documentation. inst/archive includes Wolfgang’s audit notes.

==========BELOW IS ORIGINAL README CONTENT============= eset74.rda ========== “eset”: exprSet with 4224 genes and 74 samples (renal cell cancers). Normalized with vsn. The most interesting pheno-variables are

• Subtype
• rf.survival, progress
• survival.time, died
• and the genetic aberrations

cloneanno.rda

clone annotations. data.frame with 4224 rows (yeah, I know, it should be an annotation package…)

colnames(cloneanno) [1] “plate” “SrcRow” “SrcCol” “imageid” “AccNumber” [6] “spot1” “spot2” “description” “vendor” “chromosome” [11] “llchromosome” “cytoband”

For the raw data and the preprocessing:

qua.rda

Raw data. Matrix with dim(8704, 4, 175), that is 8704 spots, 4 spot statistics, 175 chips
dimnames(qua)[[2]] 1] “fg.green” “bg.green” “fg.red” “bg.red”

spotanno.rda

Spot annotation. data.frame with 8704 rows colnames(spotanno) [1] “Block” “Row” “Column” “AccNumber” “Name” “SrcPlt” [7] “SrcRow” “SrcCol” “vendor” “ImageID” “probe”

hybanno.rda

Chip annotation. data.frame with 175 rows colnames(hybanno) [1] “filename” “patientid” “slideid”

see also

preproc.txt readdata.R runvsn74.R makecloneanno.R makeeset.R test.R