Affymetrix Power Tools Download
DOWNLOAD https://ssurll.com/2xUT6u
That said, did you download the software? Did you read a manual? I would guess that an average laptop should be able to handle it (unless it's a prehistoric one but you haven't specified anything about it's memory or computing power.)
All that adding the binary to your $PATH environment variable will do is make it so you can launch the program by typing just the name of the binary, instead of the entire path. For example, if a binary named samtools is in a folder that is in your $PATH environment variable, you can launch it by just typing
I have raw microarray data that comes as .cel files. Before I start analysis, I need to filter the data (background adjustment, quantile normalization, median polish probeset summarization) I am using Affymetrix Power tools to filter the data. I tried to follow the instructions on the manual but when I input in the command ->
The use of microarray technology to measure gene expression on a genome-wide scale has been well established for more than a decade. Methods to process and analyse the vast quantity of expression data generated by a typical microarray experiment are similarly well-established. The Affymetrix Exon 1.0 ST array is a relatively new type of array, which has the capability to assess expression at the individual exon level. This allows a more comprehensive analysis of the transcriptome, and in particular enables the study of alternative splicing, a gene regulation mechanism important in both normal conditions and in diseases. Some aspects of exon array data analysis are shared with those for standard gene expression data but others present new challenges that have required development of novel tools. Here, I will introduce the exon array and present a detailed example tutorial for analysis of data generated using this platform.
Description: "The Birdsuite is a fully open-source set of tools todetect and report SNP genotypes, common Copy-Number Variants (CNVs), andrare/de novo CNVs in samples processed with the Affymetrix Operatingsystem. While most of the components of the suite can be runindividually (for instance, to simply do SNP genotyping), the Birdsuiteis especially intended for integrated analysis of SNPs and CNVs."
Authors: Joshua Korn et al. (Broad Institute, MIT, ...)
Chip types: GenomeWideSNP_5 and GenomeWideSNP_6.
Operating system: Linux
URL:
What: The [Windows/MS-DOS] console'subst' utility makes a driveletter to any Windows directory, e.g. subst Y: 'C:/Documents andSettings/JohnDoe/Documents/MyResearch/Projects/aroma.affymetrix/ProjectA/'. This provides aworkaround when a pathname becomes too long for Windows. The maximumnumber of symbols in a pathname is 256, including file separators '/' or'\', but excluding the drive letter, and initial file separator (e.g."C:/"), and the string terminator ('\0'), cf. MSDN - Naming a File orDirectory. In Rv2.8.x, the limit is one symbol less, i.e. 255.
Operating system: Windows
URL:
Next download the Affymetrix Power Tools (APT) software package from -science/microarray-analysis/microarray-analysis-partners-programs/affymetrix-developers-network/affymetrix-power-tools.html. We need to log into the website to download the software (the registration is free).
A number of QC plots can be generated using the right tools. The full QC report can then be saved as PDF file and is available both for the __________, 1___________, and 2____________ on our server. Users are welcome to evaluate each QC plot by themselves using the data available on the server as input (see link at the bottom of this page)
The combination of the Affymetrix Expression and Transcription Analysis Consoles allows Windows-PC users without any knowledge of [R] to perform standard analysis of Affymetrix microarray data and obtain differential expression tables that can be used for downstream biological interpretation. Note that other more specific options and alternative analysis workflows are available with the same tools and that this tutorial is only an introduction with a selection of basic methods.
The main added value of these tools over [R] are the full range of QC plots generated and classically produced by bioinformatician experts as well as the very rapid processing of public Affymetrix CEL data (within minutes). We therefore recommend exploring the EC and TAC tools and associate them to IPA and other downstream tools allowing biological evaluation of public microarray data. 5376163bf9
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