CAPweb

[…] tute) were spotted in triplicate on ultraGAPS slides (Corning). The probes were prepared and hybridized as previously described [27]. The data were analyzed with software developed at Institut Curie (CAPweb, http://bioinfo-out.curie.fr/CAPweb/). Cyanine-5/cyanine-3 ratios between 0.8 and 1.2 were considered as normal status and ratios >1.2 and <0.8 were considered as gains and losses, respectively […]

[…] EA for chromosome bands using the MSigDB positional gene sets , . Centroid-linkage hierarchical clustering was performed in Cluster 3.0 and visualized in TreeView . Array CGH data was normalized with CAPweb software and genomic alterations were visualized with VAMP software using the same thresholds as previously described . SNP data were normalized with Illumina Genome Studio Software v2010.1 us […]

[…] with a median of 0.5 Mb between clones. BAC clones are spotted in quadruplicate. Hybridizations were performed according to the manufacturer’s recommendations (see Additional file ).Data analysisThe CAPweb (Copy number Array analysis Platform on the web) developed by Institut Curie (CAPWeb, http://bioinfo-out.curie.fr/CAPweb/) was used for normalization (MANOR package), segmentation and smoothing […]

[…] es, Sunnyvale, CA, USA). Further data analysis and visualization of CGH profiles were carried out as described by Unger et al. [] and Bauer et al. [] using the web-based array CGH evaluation platform CAPweb [,] and the array data visualization tool VAMP []. […]

[…] e genome of each megabase. Arrays were washed and scanned using a 4000B scanner (Axon, Union City, CA, USA). Images were analyzed with the Genepix6.0 software (AxonA). Data were processed through the CAPweb platform to obtain Cy5/Cy3 fluorescence ratios and status (gained, lost, amplified or normal) for each BAC []. […]

[…] CA, USA) and acquired images were analyzed with GenePix Pro 5.1 image analysis software to perform segmentation and to determine the mean intensities for the Cy3 and Cy5 signals of each BAC clone.The CAPweb (Copy number Array analysis Platform on the web) platform developed by Institut Curie [] was used for normalization (MANOR package), gain, loss or normal clone status assignment and breakpoint […]