convertCdf: Converts a CDF into the same CDF but with another format
In affxparser: Affymetrix File Parsing SDK

Description Usage Arguments Value Benchmarking of ASCII and binary CDFs Confirmed conversions to binary (XDA) CDFs Author(s) See Also Examples

View source: R/convertCdf.R

Converts a CDF into the same CDF but with another format. Currently only CDF files in version 4 (binary/XDA) can be written. However, any input format is recognized.

1 2	convertCdf(filename, outFilename, version="4", force=FALSE, ..., .validate=TRUE, verbose=FALSE)

`filename`	The pathname of the original CDF file.
`outFilename`	The pathname of the destination CDF file. If the same as the source file, an exception is thrown.
`version`	The version of the output file format.
`force`	If `FALSE`, and the version of the original CDF is the same as the output version, the new CDF will not be generated, otherwise it will.
`...`	Not used.
`.validate`	If `TRUE`, a consistency test between the generated and the original CDF is performed. Note that the memory overhead for this can be quite large, because two complete CDF structures are kept in memory at the same time.
`verbose`	If `TRUE`, extra details are written while processing.

Returns (invisibly) TRUE if a new CDF was generated, otherwise FALSE.

Binary CDFs are much faster to read than ASCII CDFs. Here are some example for reading complete CDFs (the difference is even larger when reading CDFs in subsets):

HG-U133A (22283 units): ASCII 11.7s (9.3x), binary 1.20s (1x).
Hu6800 (7129 units): ASCII 3.5s (6.1x), binary 0.57s (1x).

The following chip types have been converted using convertCdf() and then verified for correctness using compareCdfs(): ASCII-to-binary: HG-U133A, Hu6800. Binary-to-binary: Test3.

Henrik Bengtsson

See compareCdfs() to compare two CDF files. writeCdf().

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if (require("AffymetrixDataTestFiles")) {            # START #
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chipType <- "Test3"
cdfFiles <- findCdf(chipType, firstOnly=FALSE)
cdfFiles <- list(
  ASCII=grep("ASCII", cdfFiles, value=TRUE),
  XDA=grep("XDA", cdfFiles, value=TRUE)
)

outFile <- file.path(tempdir(), sprintf("%s.cdf", chipType))
convertCdf(cdfFiles$ASCII, outFile, verbose=TRUE)

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}                                                     # STOP #
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