inst/buildScripts/chipTypes/Cytogenetics_Array/Cytogenetics_Array,ACS.R

In aroma.affymetrix: Analysis of Large Affymetrix Microarray Data Sets

if (interactive()) savehistory();
library("aroma.affymetrix");
log <- Verbose(threshold=-10, timestamp=TRUE);


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# Settings
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chipType <- "Cytogenetics_Array";

footer <- list(
  createdOn = format(Sys.time(), "%Y%m%d %H:%M:%S", usetz=TRUE),
  createdBy = list(
    fullname = "Henrik Bengtsson", 
    email = sprintf("%s@%s", "henrik.bengtsson", "aroma-project.org")
  ),
  srcFiles = list()
);


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# Get required annotation files
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cdf <- AffymetrixCdfFile$byChipType(chipType);
print(cdf);

ptb <- AffymetrixProbeTabFile$byChipType(chipType);
print(ptb);



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# Allocate aroma cell sequence file
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acs <- AromaCellSequenceFile$allocateFromCdf(cdf, tags="HB20090519");
print(acs);


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# Import data from the Affymetrix probe-tab file (contains only PMs)
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importFrom(acs, ptb, verbose=log);

# Only for chip types with MMs:
# Infer MM from PM sequences?  Will give an error if no MMs
# inferMmFromPm(acs, cdf=cdf, verbose=log);