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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


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