Introduction to the xps Package: Comparison to Affymetrix Power Tools (APT)
نویسنده
چکیده
The aim of this document is to compare the results obtained with package xps to the results obtained with Affymetrix Power Tools (APT version apt-1.10.2). For this purpose the Exon Array Data Set ”Tissue Mixture” will be used, which can be downloaded from the Affymetrix web-site for expression arrays ”Human Genome U133 Plus 2.0”, ”Human Gene 1.0 ST” and ”Human Exon 1.0 ST”, respectively. First, APT and xps will be compared for each array type seperately, then the results obtained with the different arrays will be compared to each other for both APT and xps. To speed up analysis only two human tissues will be used, namely breast and prostate.
منابع مشابه
Package ‘ xps ’
Description The package handles pre-processing, normalization, filtering and analysis of Affymetrix GeneChip expression arrays, including exon arrays (Exon 1.0 ST: core, extended, full probesets), gene arrays (Gene 1.0 ST) and plate arrays on computers with 1 GB RAM only. It is an R wrapper to XPS (eXpression Profiling System), which is based on ROOT, an object-oriented framework developed at C...
متن کاملAffyPipe: an open-source pipeline for Affymetrix Axiom genotyping workflow
UNLABELLED The Affymetrix Axiom genotyping standard and 'best practice' workflow for Linux and Mac users consists of three stand-alone executable programs (Affymetrix Power Tools) and an R package (SNPolisher). Currently, SNP analysis has to be performed in a step-by-step procedure. Manual intervention and/or programming skills by the user is required at each intermediate point, as Affymetrix P...
متن کاملSScore: an R package for detecting differential gene expression without gene expression summaries
SUMMARY SScore is an R package that facilitates the comparison of gene expression between Affymetrix GeneChips using the S-score algorithm. The S-score algorithm uses probe level data directly to assess differences in gene expression, without requiring a preliminary separate step of probe set expression summary estimation. Therefore, the algorithm avoids introduction of error associated with th...
متن کاملShelf-life estimation of recombinant hepatitis B vaccine using R software in comparison with WHO manual protocol
Introduction: Pharmaceutical companies as well as food and cosmetics manufacturers are legally required to provide a shelf-life label on their products packaging as part of their stability study report. There are different recommended software like R software package and SAS which can perform as shelf-life estimating tools for analyzing the data achieved by the stability testing of drugs and va...
متن کاملFamily-Based Benchmarking of Copy Number Variation Detection Software
The analysis of structural variants, in particular of copy-number variations (CNVs), has proven valuable in unraveling the genetic basis of human diseases. Hence, a large number of algorithms have been developed for the detection of CNVs in SNP array signal intensity data. Using the European and African HapMap trio data, we undertook a comparative evaluation of six commonly used CNV detection s...
متن کامل