ADaCGH: analysis of data from aCGH

	Bioinformatics Unit - CNIO
	ADaCGH

ADaCGH: analysis of data from aCGH (v.20070605)

ADaCGH is a web tool for the analysis of aCGH data sets. We focus on calling gains and losses and estimating the number of copy changes.

ADaCGH will continue being maintained, but is deprecated. Our new tool for CGH and CNV is WaviCGH .

To use ADaCGH provide either one or two files. If you only provide one file, that file must contain also coordinates (location information) of each of the genes/clones. If you provide two different files, one must contain the the aCGH data themselves and another one the mapping of those genes/clones to positions in chromosomes.

Input files (help)

Two files: (aCGH data + coordinates)

Genomic data file:
Coordinate/position information file:

One file (First column are names, next three columns are coordinates.)

Genomic data + coordinate information file:

Centering

Median centering Mean centering None

Centering is done on a per-array basis. Some methods do require that data be centered, and for others centering simplifies interpretation. See further details in the help

Method (help)

CBS: Olshen & Venkatraman's circular binary segmentation (CBS).

HMM: Fridlyand et al.'s homogeneous Hidden Markov Model (HMM).

BioHMM: Marioni et al.'s non-homogeneous HMM. This is the only method that incorporates distance between probes

CGHseg: Piccard et al.'s CGH segmentation.

minDiff

GLAD: Huppé et al.'s Gain and Loss Analysis of DNA (GLAD).

Wavelet smoothing (Wavelets): Hsu et al.'s wavelet-based smoothing.

minDiff

Use mergeLevels algorithm? (help) (New!!) Yes No

Price-Smith-Waterman (PSW): Price et al. method for aCGH using Smith and Waterman's algorithm.

Permutation test

Number of permutations

Plotting

Largest p-value shown

Analysis of copy errors (ACE): Lingjaerde et al.'s CGH Explorer.

(desired) FDR

Minimal common regions (help) (New!!)

gapAllowed

alteredLow

alteredHigh

recurrence

Type of gene identifier and species (help)

To provide clickable links (that take you to IDClight the one-query-version of our IDConverter) in the results.

	Type of ID for gene names	Organism
	Affymetrix ID	Human (Homo sapiens)
	Clone ID (IMAGE Consortium)	Mouse (Mus musculus)
	GenBank Accession	Rat (Rattus norvegicus)
	Ensembl Gene	None of the above
	Unigene cluster
	RefSeq RNA
	RefSeq peptide
	HUGO Gene Name
	Entrez Gene
	CNIO ID
	None of the above

Note: Floating-point numbers, such as 0.001, can be specified as either "0.001", "1e-3" or "1E-3" (without the "", of course). Anything else will produce an error.

Click "Submit" to send the data to the server and start execution. If the servers are too busy, you will be asked to try again later.

Help

Citing ADaCGH

Diaz-Uriarte, R and Rueda, OM. "ADaCGH: A Parallelized Web-Based Application and R Package for the Analysis of aCGH Data", PLoS ONE, 2007, 2 (8): e737

Send comments to webmaster