APT, developed by Affymetrix, are a set of cross-platform command line programs that implement algorithms for analyzing and working with Affymetrix GeneChip® arrays. APT programs are intended for "power users" who prefer programs that can be utilized in scripting environments and are sophisticated enough to handle the complexity of extra features and functionality.
Two of the most popular programs and their features:
apt-probeset-summarize: An application for analyzing expression (i.e., U133 and Exon Arrays). Features include:
- Multiple summarization methods like PLIER, RMA, MAS5, DABG, and IterPLIER
- Sketch quantile normalization (saves memory)
- Lots of parameters available to power users
- Save and reuse feature effects and target normalizations
- Use meta-probeset files to group probe sets into larger probe sets (i.e., combine exons into genes)
- Can run thousands of chips in 1-2 GB of RAM by dividing job into smaller pieces
- Jobs can be split for running on cluster
- Run multiple analysis at once (i.e., Plier and RMA)
- Relatively fast and robust: process 848 Human Exon Arrays with RMA-sketch in about two days on Windows 2 GB RAM machine
apt-probeset-genotype: An application for making genotype calls using Mapping Arrays (100K, 500K, Genome-Wide SNP Arrays 5.0 and 6.0). Features include:
- Implements BRLMM, BRLMM-P and Birdseed algorithm
- Will output DM calls
- Outputs allele summaries for copynumber applications
- Lots of parameters available to power users
- Save and reuse feature effects and target normalizations
- Jobs can be split for running on cluster
- Relatively fast and robust: BRLMM on 96 250K Sty arrays in about 60 minutes on Windows 2 GB RAM machine
Programs Location on Helix
/usr/local/apt/bin
Library Location on Helix
/usr/local/apt/library
Contact staff@helix.nih.gov if you need extra libraries installed on Helix
Version
1.10.2
Sample Session
Sample sessions for the above two most popular programs are given below. Sample input files can be copied from /usr/local/apt/sample.
apt-probeset-genotype sample session
% cd /home/user/apt-genotype
% cp /usr/local/apt/sample/genotype/*.zip .
% unzip '*.zip'
% /usr/local/apt/bin/apt-probeset-genotype -o results_dir -c \ CD_Mapping250K_Sty_rev4/Full/Mapping250K_Sty/LibFiles/Mapping250K_Sty.cdf --chrX-snps \ CD_Mapping250K_Sty_rev4/Full/Mapping250K_Sty/LibFiles/Mapping250K_Sty.chrx \ 500K_data/chip_data/Sty/Sty*/*.CEL
Beginning analysis of 48 cel files.
Opening layout file: CD_Mapping250K_Sty_rev4/Full/Mapping250K_Sty/LibFiles/Mapping250K_Sty.cdf
Reading 238378 probesets.........................................Done.
Kept 238378 probesets.
Read 4659 ChrX SNPs from chrX SNPs file CD_Mapping250K_Sty_rev4/Full/Mapping250K_Sty/LibFiles/Mapping250K_Sty.chrx (v2)
Doing 1 iteration.
Reading 48 cel files................................................Done.
Using gender method dm-chrX-het-rate for genotype calling.
Computing prior with: 10000 initial snps.
5647 of 10000 (56.47%) of SNPs had at least 2 observations per genotype.
5647 SNP clusters used to generate prior.
Processing 238378 probesets in this iteration (1 thru 238378 out of 238378 total).
Processing probesets.........................................Done.
Releasing memory for next iteration
Done with block iterations.
Flushing output reporters. Finalizing output.
Cleaning up.
Done.
Run took approximately: 203.46 minutes.
apt-probeset-summarize sample session 1:
% cd /home/user/apt-summarize
% cp /usr/local/apt/sample/summarize/*.zip .
% unzip '*.zip'
% /usr/local/apt/bin/apt-probeset-summarize -a rma-sketch -a plier-mm-sketch \
-d CD_HG-U133_Plus_2/Full/HG-U133_Plus_2/LibFiles/HG-U133_Plus_2.cdf \
-o outputdir *.CEL
Opening cdf file: HG-U133_Plus_2.cdf
Reading 54675 probesets.........................................Done.
Kept 54675 probesets.
Expecting 1 iteration.
Doing iteration: 1
Reading 33 cel files.................................Done.
Processing Probesets......................Done.
Releasing memory for next iteration.
Flushing output reporters. Finalizing output.
Done.
Done.
Run took approximately: 11.01 minutes.
apt-probeset-summarize sample session 2:
-p /YourPathToLibraryFile/HuEx-1_0-st-v2.r2.pgf \
-c /YourPathToLibraryFile/HuEx-1_0-st-v2.r2.clf \
-b /YourPathToLibraryFile/HuEx-1_0-st-v2.r2.antigenomic.bgp \
--qc-probesets /YourPathToLibraryFile/HuEx-1_0-st-v2.r2.qcc \
-m /YourPathToLibraryFile/HuEx-1_0-st-v2.r2.dt1.hg18.core.mps \
-a rma-bg,pm-gcbg,sea \
-o /PathToOutput/outfile \
--cel-files /PathOfCelfiles/celfiles.txt
The 'celfiles.txt' at last line contains the full path cel file names, for example:
--------------- Content of celfiles.txt ----------------------
cel_files
/data/maoj/apt/wuti/test1/PLX090227_NuGen_WT_PAX_GR_1.CEL
/data/maoj/apt/wuti/test1/PLX090227_NuGen_WT_PAX_GR_2.CEL
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Documentation
https://www.affymetrix.com/support/developer/powertools/changelog/index.html
