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Affymetrix Integration
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Expression Data Input |
Using the Affymetrix API |
Data may be read directly from an Affymetrix data base using the Affymetrix API. |
From ASCII/Excel files. |
Affymetrix can also be presented to Genetrix in a text file or an Excel spreadsheet. |
Probe modeling |
Genetrix include algorithms based on the dChip. RMA and Probe Profiler approaches to probe set modeling, that provide increased signal to noise discrimination by analyses of patterns of probe hybridization across multiple chips. |
Annotations |
NetAffx data |
Genes annotations include the comprehensive annotations provided for each probe set on the Affymetrix NetAffx site. |
Probe set |
Replicates |
Genetrix accommodates the Affymetrix chip set design which includes multiple probe sets for many genes, by providing a flexible means of selecting or combining data from replicates. |
View probe specific data |
Hybridization intensities from individual PM and MM probes can be viewed. If probe modeling has been used, the probe weights can be plotted along with the PM-MM values. A variety of graphics are used to visualize probe performormance. |
Probe alignment |
Probe sequences, obtained from Affymetrix annotation files, can be aligned to genomic sequence data for a gene to determine the location of the targets at the nucleotide level. |
SNP arrays |
Data input |
SNP data from Affymetrix SNP arrays can be input and associated with expression and covariate data. |
SNP information |
Annotations for individual SNPs, including race-specific alleles frequences derived from the Affymetrix annotation file, can be viewed. |
Chromosomal mapping |
SNPs can be mapped to a chromosomal ideogram. |
Loss of heterozygosity |
Regions of LOH can be viewed on the chromosomal ideogram, either for a single sample or aggregated over multiple samples. |
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