Uset Guide

AffyMAPSDetector User Guide

Introduction

AffyMAPSDetector stands for Affymetrix MicroArray Probe SNP Detector. It detects the presence of SNPs (Single Nucleotide Polymorphism) in the probes of Affymetrix GeneChip^TM expression arrays. However, it can be used to characterize any GeneChip^TM with respect to SNPs for which NCBI fully supports gene and SNP annotations (i.e. the organism for which GeneChip^TM is desinged and that organism's genome exists in NCBI nucleotide and SNP database).

AffyMAPSDetector requires two ASCII text files as input data sources: “NetAffx Annotation File” and “Sequence File". Both of these files are available for download from the Affymetrix support page under “NetAffx Annotation File” and “Sequence Files” respectively.

Affymetrix provides the Chip Definition File (CDF file) and the NetAffx^TM Annotation files (Gene Information File - GIF & Probe set Information File - PIF) for each GeneChip^TM. The CDF file contains GeneChip^TM design and layout details whereas NetAffx^TM annotation files provide detailed information about the sequence, genomic location & function of the genes of the corresponding probe sequences, those are laid-out on the chip. In their current implementation, these files do not include SNP information but provide useful links - Representative Public ID and Entrez Gene a.k.a LocusLink. AffyMAPSDetector uses these links to find SNP-containing probes in a given Affymetrix GeneChip^TM. One of the main goals of AffyMAPSDetector is to make expression array chips SNP sensitive, so that anomalies in the expression signal at SNP locations can be carefully screened, thereby improving data pre-processing methods and subsequent post-experiment analyses. The SNP detection results from AffyMAPSDetector can be effectively utilized in the microarray experiment design as well as in the expression array data analysis.

How To

First, download and install AffyMAPSDetector..
Obtain Gene Information File (NetAffx Annotation File) and Probeset Information File (Sequence File) from NetAffx^TM analysis center (Human Genome Array). Both are ASCII text files (tab/comma delimited). To download these files you would need to register with Affymetrix (registration is free).
Download sample gene information file (GIF file) for HG-U95Av2 gene chip. The only required columns of information in this file are Representative Public ID and Locus Link (now called Entrez Gene). AffyMAPSDetector doesn't need rest of the columns. This file can be quite large and can become AffyMAPSDetector performance bottleneck. To improve AffyMAPSDetector performance, one can retain the columns of information that are needed and delete rest of the columns.
Download sample probeset information file (PIF file) for HG-U95Av2 gene chip.
Finally, before running AffyMAPSDetector make sure your computer is connected to the internet.

To launch AffyMAPSDetector, do the following steps:

Load Files: Click on the File->Load... menu item. This would launch File Loader Wizard that would further guide you to load the GIF and PIF. There are 3 wizard steps:

Step 1: Select the gene information file data field separator character. Browser to the GIF location and specify data columns corresponding to Representative Public ID and LocusLink ID (Entrez Gene). Also, select the GeneChip organism.
Step 2: Load probeset information file and specify data column corresponding to probeset id (probeset name), x/y location of the probe on the chip, interrogation position, and probe's sequence.
Step3 : At this step you can specify names of the five output files that AffyMAPSDetector generates during the process of SNP detection. These files are: (1) Probes that contain SNP at 13^th or any other position in the probe sequence. (2) Probes which do not contain SNP. (3) Genes for which Entrez Gene ID is not provided by NetAffx^TM in the gene annotation file. (4) mRNA sequence of the genes extracted from web. (5) Detailed SNP info extracted from web for each gene. Note that each of these files is a “tab/comma delimited” ASCII text file.

View Files: You can view the contents of either GIF or PIF by clicking on the appropriate item under View menu.

Start SNP Detection: Once GIF and PIF are loaded, process of SNP detection can be started by clicking on the File->Start menu item.
Depending on the number of genes on the GeneChip^TM, machine's processing power, internet connection speed, and network load on the NCBI website the timings of SNP detection for the entire chip can vary significantly.
Stop SNP Detection: You can stop the SNP detection process whenever is desired. There are two options under File->Stop to do so:
- Halt: to temporarily stop the process of SNP detection.
- Stop: to stop the process of SNP detection all together.

Note that AffyMAPSDetector does not override/append an existing output file.