Tilescope: online analysis pipeline for high-density tiling microarray data

Table 1 Feature comparison between tiling microarray data analysis software*

	Tilescope	Bioconductor^†	TAS^‡	MAT^§	TileMap
Implementation	Web	R packages	Standalone	Standalone	Standalone
Graphic user interface	√	×	√	×	×
Intended usage
Transcription data	√	√	√	×	√
ChIP-chip data	√	√	×	√	√
Applicable array platform
Affymetrix	√	√	√	√	√
NimbleGen	√	×	×	×	×
Data normalization
Mean/median	√	~	√	/	×
Loess	√	~	×	/	×
Quantile	√	~	×	/	√
Feature identification
Max gap and min run	√	~	√	/	√
Iterative peak identification	√ (new)	×	×	/	×
Hidden Markov model	√	~	×	/	√

*Only programs explicitly applicable to high-density tiling microarray data were considered. The websites of the compared programs are listed as follows: Tilescope at [35]; Bioconductor at [37]; TAS at [38]; MAT at [39]; TileMap at [40]. ^†Strictly speaking, Bioconductor is not a ready-to-run program. It is a collection of software packages/libraries written in R. As a tool box, the analysis methods that it provides need to be written in an R program to run. ^‡TAS is previously known as GTRANS. ^§MAT standardizes the probe value through the probe model, which obviates the need for sample normalization. Comparison symbols used in the table: √, available; ×, not available; ~, available but need to be programmed; /, not applicable.

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