R version 4.5.0 RC (2025-04-04 r88112 ucrt) -- "How About a Twenty-Six"
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> library("aroma.apd")
Loading required package: affxparser
aroma.apd v0.7.1 successfully loaded. See ?aroma.apd for help.
> 
> # Float precision
> .Machine$float.eps <- (2^((8-4)*8)*.Machine$double.eps)
> tol <- .Machine$float.eps ^ 0.5
> 
> 
> # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
> # 1. Create an Affymetrix Probe Signal (APD) file for a
> #    'Mapping50K_Hind240' with 1600-by-1600 probes.
> # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
> chipType <- "Mapping50K_Hind240"
> nbrOfCells <- 1600^2
> 
> pathname <- paste(tempfile(), "apd", sep=".")
> createApd(pathname, nbrOfCells=nbrOfCells, chipType=chipType)
> 
> # File size
> cat("File name:", pathname, "\n")
File name: D:\temp\2025_04_06_19_05_17_23833\RtmpSE8LLX\file284283cf06b13.apd 
> cat("File size:", file.info(pathname)$size, "bytes\n")
File size: 10244369 bytes
> cat("APD header:\n")
APD header:
> header <- readApdHeader(pathname)
Warning messages:
1: In readChar(con = con, nchars = 64) :
  truncating string with embedded nuls
2: In readChar(con = con, nchars = 16) :
  truncating string with embedded nuls
> print(header)
$creator
[1] "R package aroma.snp by Henrik Bengtsson"

$dataType
[1] "float"

$bytesPerCell
[1] "4"

$RStorageMode
[1] "double"

$chipType
[1] "Mapping50K_Hind240"

$nbrOfProbes
[1] 2560000

> 
> 
> # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
> # 2. Update the signals for a subset of probes
> # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
> cells <- c(1, 1100:1120, 220:201, 998300:999302)
> signals <- log(cells+1, base=2)  # Fake signals
> updateApd(pathname, indices=cells, data=signals)
Warning messages:
1: In readChar(con = con, nchars = 64) :
  truncating string with embedded nuls
2: In readChar(con = con, nchars = 16) :
  truncating string with embedded nuls
> 
> 
> # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
> # 3. Re-read the signals for a subset of probes
> # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
> apd <- readApd(pathname, indices=cells)
Warning messages:
1: In readChar(con = con, nchars = 64) :
  truncating string with embedded nuls
2: In readChar(con = con, nchars = 16) :
  truncating string with embedded nuls
> 
> # Signals in APD files are stored as floats (since this is
> # the precision in CEL files).
> stopifnot(all.equal(signals, apd$intensities, tolerance=tol))
> 
> 
> # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
> # 4. Re-read the signals for a subset of probes
> # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
> if (require("affxparser")) {
+   cdfFile <- findCdf(chipType)
+   if (length(cdfFile) > 0) {
+ 
+     apd <- readApdUnits(pathname, units=100:104)
+ 
+     # Sample new data (with one decimal precision)
+     apd2 <- lapply(apd, function(unit) {
+       lapply(unit, function(groups) {
+         n <- length(groups$intensities)
+         values <- as.integer(runif(n, max=655350))/10
+         list(intensities=values)
+       })
+     })
+ 
+     # Update APD file with new data
+     updateApdUnits(pathname, units=100:104, data=apd2)
+ 
+     # Re-read data to verify correctness
+     apd <- readApdUnits(pathname, units=100:104)
+ 
+     # Signals in APD files are stored as floats (since this is
+     # the precision in CEL files).
+     stopifnot(all.equal(apd2, apd, tolerance=tol))
+   } # if (length(cdfFile) > 0 ...)
+ } # if (require("affxparser"))
> 
> 
> # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
> # 4. Clean up
> # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
> file.remove(pathname)
[1] TRUE
> 
> proc.time()
   user  system elapsed 
   0.34    0.12    0.92