MANUAL: apt-cel-transformer (apt-1.12.0)

Contents

Options:

apt-cel-transformer - Utility program for taking cel files and converting them
using a ChipStream path and saving the results to a modified set of cel files.
An example would include rma background subtracting and normalizing a set
of cel files that could then be used in another application without those
capabilities.

 *Warning* - If the output directory is the same as the input directory the
the original cel files will be overwritten with the transformed ones.

A chipstream pathway is specified by a comma separated list of transformations
with specific parameters passed as key value pairs. For example:
rma-bg,quant-norm.usepm=true.sketch=50000 -> rma background subtract and then
                                             quantile normalize using only PM
                                             probes and a sketch size of 50K
rma-bg,med-norm -> rma background subtraction and then median normalization.

usage:
   apt-cel-transformer -d chip.cdf -c rma-bg,quant-norm.sketch=50000 -o out-dir \ 
      celFile1.cel celFile2.cel ... celFileN.cel


options:
   -h, --help                           This message. [default 'false'] 
   -v, --verbose How verbose to be with status messages 0 -
                          quiet, 1 - usual messages, 2 - more
                          messages. [default '1'] 
     --target-sketch File specifying a target distribution to 
                          use for quantile normalization. [default 
                          ''] 
     --a5-target-sketch File specifying an target distribution to
                          use for quantile normalization in A5 
                          format. [default ''] 
   -c, --chipstream String representing tranformation desired.
                          For example: 'quant-norm.sketch=50000' does
                          a quantile normalization using 50000 
                          points. [default ''] 
     --probe-norm-file File specifying index of probes (1 based) 
                          to use for normalization. [default ''] 
     --disk-cache Size of memory cache when working off disk
                          in megabytes. [default '50'] 
   -d, --cdf-file File defining probe sets [default ''] 
     --clf-file File defining probes [default ''] 
     --kill-list File defining probes to remove [default ''] 
     --pgf-file File defining probe sets [default ''] 
     --spf-file File defining probe sets [default ''] 
     --write-sketch Write the quantile normalization
                          distribution (or sketch) to a file in
                          output-dir for reuse with target-sketch
                          option. [default 'false'] 
     --a5-write-sketch Write the quantile normalization
                          distribution (or sketch) to a file in
                          output-dir for reuse with target-sketch
                          option. [default 'false'] 
     --force Disable chip type checks. [default 'false'] 
   -o, --out-dir Directory to write result files into.
                          [default '.'] 
     --temp-dir Directory for temporary files when working
                          off disk. Using network mounted drives is
                          not advised. When not set, the output 
                          folder will be used. [default ''] 
     --version Display version information. [default
                          'false'] 

Frequently Asked Questions

Q. What is a probe_id?

A. See the FAQ item on probe IDs for more info.

Q. The normalized results from apt-cel-transformer appear to be ignoring the --probe-norm-file option:

    apt-cel-transformer \
        --probe-norm-file probe_ids.txt \
        -c rma-bg,quant-norm.sketch=0.usepm=true.bioc=true \
        -o transformed \
        *.CEL

A. The "usepm=true" is trumping the use of the --probe-norm-file specification as both are telling the quantile normalization to use a subset of the probes.

Q. I do not have a CDF file for the arrays I want to process. (WT based arrays have PGF/CLF files rather than CDF files)

A. You can still use this tool. Omit the CDF command line arg. Note that you will not be able to use ChipStream methods which require chip layout information. Most notably you cannot use the rma-bg method and you cannot use the pm-only option to quant-norm.

Q. How is the mask section in the CEL file used?

A. It is not. The contents of this section of the CEL file are ignored.

Q. Where can I get more information about what can be provided with --chipstream?

A. See the "Data transformations" section of the options in the apt-probeset-summarize manual. You can use the --explain option to apt-probeset-summarize to get further information on each of the transformation methods.

Q. Can I compute gc-RMA values using APT.

A. No. APT (specifically apt-probeset-summarize) does not currently implment gc-RMA.

Q. Wild cards do not work on windows. For example:

    apt-cel-transformer ... *.CEL

A. APT relies on the command shell to do the wild card expansion (ie bash shell on NIX systems). The windows shell does not do wild card expansion, so there is no wild card expansion for APT when run from the windows shell. You may want to try a different windows shell or perhaps bash via cygwin.