VIGNETTES: Using GC Correction (GCCN) and Space Transformation (SST) algorthms with apt-probeset-summarize




This vignette describes how to use apt-probeset-summarize to apply RMA summarization with GC Correction (GCCN) and Space Transformation (SST) algoritms.

Transforming a single HTA cel file

This should give fold change which compares well with other techniques, like Next Gen Sequencing.

apt-probeset-summarize  \
      --store-duplicate-probes \
      -a gc-sst-rma-sketch \
      -p HTA-2_0.r1.pgf \
      -c HTA-2_0.r1.clf \
      -o my_output_folder \ 
      --cel-files cel_files.txt \
      --qc-probesets HTA-2_0.r1.qcc

NOTE: qc-probesets file is optional. Any probes in probe sets called out in the qcc file will be excluded from GCCN and SST

The QCC file is a tab delimited text file with the following columns:

Custmization Command Line Options

The following command line shows customization of the opttions for GC correction and Space Transformation:

apt-probeset-summarize \
      --store-duplicate-probes \
      -a gc-correction \
              .cel_out=false, \
         scale-intensities \
              .floor=1 \
              .low=20 \
              .high=50000 \
              .ceiling=1000000 \
              .low_pct=0.02 \
              .high_pct=0.98 \
              .cel_out=false, \
         rma-bg, \
         quant-norm.sketch=0.usepm=true.bioc=true, \
         pm-only, \
         med-polish \
      -p HTA-2_0.r1.pgf \
      -c HTA-2_0.r1.clf \
      -o my_output_folder \
      --cel-files cel_files.txt