Topics

  • What is the method of normalisation used in Fish and Chips?
  • LOWESS:
    Linear bias and non-linear bias (saturation, background or print-tip effect) are often observed in micro-array datasets. Such bias were corrected by normalizing all datasets with a LOWESS (Locally WEighted Scatter plot Smoothing) procedure [1] implemented in the statistical software package R [2]. We specifically use a channel by channel procedure [3], each array being individually normalized to the median profile of all arrays of the considered dataset.

    [1] Yang YH, Dudoit S, Luu P, Lin DM, Peng V, Ngai J, Speed TP: Normalization for cDNA microarray data: a robust composite method addressing single and multiple slide systematic variation. Nucleic Acids Res 2002, 30:e15.

    [2] Ihaka R, Gentleman R: A language for data analysis and graphics. J Comput Graph Statist 1996, 5:299-314.

    [3] Workman C, Jensen LJ, Jarmer H, Berka R, Gautier L, Nielser HB, Saxild HH, Nielsen C, Brunak S, Knudsen S: A new non-linear normalization method for reducing variability in DNA microarray experiments. Genome Biol 2002, 3(9):research0048.

  • What is the cluster analysis used in Fish and Chips?
  • We used Hierarchical clustering methods described in Eisen et al. (1998) PNAS 95:14863.
    We ajusted data (log transform and median center genes) before hierarchical clustering (uncentered correlation, average linkage).
    Download Cluster (Eisen)

  • How to read cluster files (.cdt, .gtr, .atr)?
  • You must use Treeview:
    Graphically browse results of clustering and other analyses from Cluster.
    Supports tree-based and image based browsing of hierarchical trees.
    Download JavaTreeview
    Download Treeview (Eisen)

    Note for french users:
    If your decimal symbol for numbers is coma, you must change in point to read Fish and Chips cluster files (Control Panel, Regional Options, Numbers, Decimal symbol).

  • What is the method used to annotate gene clusters?
  • We used a statistical approache (Fisher's exact test) on gene ontology (GO) annotations to determine statistically significant terms in gene clusters.
    GO tools used in Fish and Chips:
    - GoMiner
    - EASE