Open HenrikBengtsson opened 8 years ago
This originates from affxparser::cdfHeaderToCelHeader()
;
> affxparser::cdfHeaderToCelHeader
> affxparser::cdfHeaderToCelHeader
function (cdfHeader, sampleName = "noname", date = Sys.time(),
..., version = "4")
{
version <- match.arg(version)
celHeader <- list()
celHeader$version <- version
celHeader$cols <- cdfHeader$cols
celHeader$rows <- cdfHeader$rows
celHeader$total <- celHeader$rows * celHeader$cols
celHeader$chiptype <- cdfHeader$chiptype
celHeader$algorithm <- "NoAlgorithm"
pd <- packageDescription("affxparser")
creator <- sprintf("Creator:%s;Version:%s;", pd$Package,
pd$Version)
celHeader$parameters <- paste(creator, sep = "")
cols <- celHeader$cols
rows <- celHeader$rows
datHeader <- list(pixelRange = "[0..65535]", sampleName = sampleName,
CLS = cols, RWS = rows, XIN = 0, YIN = 0, VE = 0, scanTemp = "",
laserPower = "", scanDate = format(date, "%m/%d/%y %H:%M:%S"),
scanner = list(id = "", type = ""), chipType = celHeader$chiptype)
datHeader <- .wrapDatHeader(datHeader)
header <- sprintf("Cols=%d\nRows=%d\nTotalX=%d\nTotalY=%d\nOffsetX=0\n
OffsetY=0\nGridCornerUL=0 0\nGridCornerUR=%d 0\nGridCornerLR=%d %d\n
GridCornerLL=0 %d\nAxis-invertX=0\nAxisInvertY=0\nswapXY=0\nDatHeader=%s\n
Algorithm=%s\nAlgorithmParameters=%s\n",
cols, rows, cols, rows, cols, cols, rows, rows, datHeader,
celHeader$algorithm, celHeader$parameters)
celHeader$header <- header
celHeader$cellmargin <- 2
celHeader$noutliers <- 1
celHeader$nmasked <- 1
celHeader
}
<environment: namespace:affxparser>
UPDATE: There are several other methods in aroma.affymetrix that uses cdfHeaderToCelHeader()
; should they also be "fixed".
It looks like
convertToUnique()
for AffymetrixCelSet writes CEL files that have a creation timestamp in the header. Instead of creating a timestamp for when the file was created, it's / it may be better to have it inherit the timestamp from the source CEL file.