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PLATA specifications


Unique identifier OMICS_23179
Alternative name Probe Level Alternative Transcript Analysis
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Python
Computer skills Advanced
Version 1.0
Stability Stable
Numpy, Scipy, Pyrex, Pytables, Pyx, MAT
Maintained Yes


  • Primates
    • Homo sapiens
  • Rodents
    • Mus musculus



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  • person_outline Chris Burge <>
  • person_outline Rickard Sandberg <>
  • person_outline Philip Sharp <>

Publication for Probe Level Alternative Transcript Analysis

PLATA in publications

PMCID: 5445373
PMID: 28545391
DOI: 10.1186/s12859-017-1687-8

[…] a linear model to the observed data aiming to identify non-zero interaction terms between the sample groups and the exons. however, it has been argued that the anosva method performed poorly []. the probe level alternative transcript analysis (plata) method is based on the normalization of probe level intensities: first the probe-wise intensities, using gene level summarized values, […]

PMCID: 2728531
PMID: 19607685
DOI: 10.1186/gb-2009-10-7-r77

[…] non-zero interaction terms between sample groups and exons [], but this approach did not show favourable performance in the evaluations carried out by affymetrix []. recently, a procedure called plata (probe-level alternative transcript analysis) was introduced, which normalizes the expression intensities first probe-wise using the gene-level summary values and then compares the group means […]

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PLATA institution(s)
Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA; Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA; Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA, USA
PLATA funding source(s)
Supported by the Knut and Alice Wallenberg Foundation; the Cancer Research Institute; the Gina De Felice and Robert M. Lefkowitz (1975) Fund; United States Public Health Service grants RO1-GM34277 from the National Institutes of Health, PO1-CA42063 and U19 AI056900 from the National Cancer Institute to PAS and partially by Cancer Center Support (core) grant P30-CA14051 from the National Cancer Institute; and by R01- HG002439 from the NHGRI.

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