From LipidomicsWiki

Contents 1 Introduction: 2 Input: 3 Output: 4 Processing: 5 Literature: 6 Proposals and discussion points

Introduction:

At the Institute for Clinical Chemistry ( P01 ) ChipInspector is used for standard analysis. ChipInspector is part of a software bundle from Genomatix, containing also a pathway analysis software called BiblioSphere.

One of the main features of ChipInspector can be found when analyzing Affymetrix microarrays. In contrast to other processing approaches for Affymetrix it doesn’t compute summary-values or fits on PM or MM-probes before computing differential expression. Instead it performes a statistical test for every PM-probe. A gene or transcript will be called differential expressed, if a user-defined number of differential expressed probes has been found. However it is also possible to analyze microarrays with one-probe-per-gene approaches( e.g. agilent) as well, by setting this treshold to one.

Input:

Typical output files for the supported array platforms (e.g. cel-files when considering affymetrix-arrays) .

Output:

A list of differential expressed genes and some information e.g: gene symbols, accession numbers of the possible transcrips, log fold changes and the false discovery rate (FDR)
Also special output-format for the Genomatix-Software Bibliosphere can be generated.

Processing:

ChipInspector has a tight preprocessing-pipeline, which cannot be changed by the user. Normalization is done by scaling to a common mean.
For computation of differential expression Genomatix uses a T-test with a permutated artificial background. This algorithm is based on the significance analysis of microarrays- algorithm ( Tusher 2001 ). In contrast to the original algorithm it always uses a paired t-statistic. In case of unpaired samples every sample of one group will be paired with every sample from the other group.

Literature:

Tusher VG, Tibshirani R, Chu G. Signifcance analysis of microarrays applied to the ionizing radiation response. PNAS. 2001;98(9):5116-5121.

Proposals and discussion points

Write here any proposals and discussion points you may have.

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