Probe filtering software tools | DNA methylation microarray data analysis
Several reasons can explain the generation of artifactual data. For example, the scanner can encounter some difficulties to correctly read the signal for some probes owing to their low intensities or to some spatial artifacts on the array. This problem translates as a high detection P-value (i.e. a low quality signal) for the probes concerned. It is therefore strongly recommended to filter out probes displaying a high detection P-value (e.g. >0.05) before performing downstream analyses. This problem is common to all microarray platforms.
Allows users to collect, manage, and effectively analyze data from microarray experiments. TM4 Microarray Software Suite is composed of a set of four tools: Madam, Spotfinder, Midas and MeV. It offers functions that allow users to record their experimental parameters and data; permit researchers to load the output of a microarray scanning operation and to adjust the placement of each grid cell manually allow for accurate spot detection.
Offers an intuitive user interface and built-in workflows for a variety of genomic applications that guide researchers though every step of the analysis process. Partek Genomics Suite gives biologists, bioinformaticists, and statisticians a single, integrated solution for trustworthy results with a user-friendly interface, comprehensive workflows, and ability to support all next generation sequencing, microarray, and qPCR platforms.
Provides several basic functions for filtering genes from a microarray dataset. genefilter is an R package to find genes whose expression profile is similar to that of specified genes. This tool can also generate diagnostic plots to help visualizing this association.
A suite of computational tools that incorporate state-of-the-art statistical techniques for the analysis of DNAm data. minfi provides methods for preprocessing, quality assessment and detection of differentially methylated regions from the kilobase to the megabase scale. Several preprocessing algorithms are available and the infrastructure provides a convenient way for developers to easily implement their techniques as Bioconductor tools. By making SNP annotation available, users can choose to be cautious about probes that may behave unexpectedly due to the inclusion of a SNP in the probe sequence. minfi is unique in that it provides both bump hunting and block finding capabilities, and the assessment of statistical significance for the identified regions. Finally, because the package is implemented in Bioconductor, it gives users access to the countless analysis and visualization tools available in R.
A package that provides classes for holding and manipulating Illumina methylation data. Based on eSet, it can contain MIAME information, sample information, feature information, and multiple matrices of data. An ``intelligent'' import function, methylumiR can read the Illumina text files and create a MethyLumiSet. methylumIDAT can directly read raw IDAT files from HumanMethylation27 and HumanMethylation450 microarrays. Normalization, background correction, and quality control features for GoldenGate, Infinium, and Infinium HD arrays are also included.
An easy-to-use application for microarray, RNA-Seq and metabolomics analysis. For splicing sensitive platforms (RNA-Seq or Affymetrix Exon, Gene and Junction arrays), AltAnalyze will assess alternative exon (known and novel) expression along protein isoforms, domain composition and microRNA targeting. In addition to splicing-sensitive platforms, AltAnalyze provides comprehensive methods for the analysis of other data (RMA summarization, batch-effect removal, QC, statistics, annotation, clustering, network creation, lineage characterization, alternative exon visualization, gene-set enrichment and more).
An R package for comprehensive analysis of DNA methylation data obtained with any experimental protocol that provides single-CpG resolution, including Infinium 450K microarray and bisulfite sequencing protocols, but also MeDIP-seq and MBD-seq.