Dear Raquel, Thanks for the report. The current pint version has been designed for and tested with aCGH probe-level data. The framework should be applicable to segmented data as well. We are now working on this, and will let you know as soon as the issue has been fixed. Note that segmentation as preprocessing is not necessarily required. The methods (pCCA/pSimCCA etc.) detect the strongest shared signal of the probes within the investigated chromosomal region. This corresponds to automatic segmentation with explicit modeling assumptions. Ordinary segmentation approaches are likely to loose information when summarizing individual probe-level observations into a single segment-level value; pint tries to avoid such information loss. Segmentation might help to avoid overfitting when sample size (number of arrays) is particularly small (compared to the number of probes within the region); otherwise we would recommend operating directly on probe-level observations with the pSimCCA method, which has proved robust to small sample sizes in our experiments. The currently implemented models (pPCA/pFA/pCCA/pSimCCA) assume approximately normally distributed data (log2 fold change values) for both gene expression and copy number mesurements. As a standard quality check, one should also confirm that the technical biases between the arrays are minimized before the analysis. with best regards Leo Lahti Aalto University School of Science and Technology tel: +358 (0)9 470 25116 Department of Information and Computer Science email: leo.lahti at tkk.fi P.O. Box 15400, FI-00076 Aalto, FINLAND http://www.cis.hut.fi/lmlahti Date: Fri, 07 May 2010 10:16:32 +0200 From: =?UTF-8?B?UmFxdWVsIE1hcnTCkmluZXogR2FyY8KSaWE=?= <rmartinezg at="" cnio.es=""> User-Agent: Thunderbird 2.0.0.24 (Macintosh/20100228) MIME-Version: 1.0 To: Mailing List Bioconductor <bioconductor at="" stat.math.ethz.ch=""> Subject: pint Content-Type: text/plain; charset=UTF-8; format=flowed Content-Transfer-Encoding: 7bit Hello! Thanks Mr. Carey for your reply. Any genes have the same values because the data are segmented. Now I need to know if the both methods pCCA and pSimCCA have any problems for work with segmented data or do not these methods work for another reason?. Thanks in advance Raquel -- ******************************************** Raquel Martinez Garcia, Graduate Student Gastrointestinal Cancer Clinical Research Unit & Structural Computational Biology Group Spanish National Cancer Research Center, CNIO Melchor Fernandez Almagro, 3. 28029 Madrid, Spain. Phone: +34 91 732 80 00 #3015 rmartinezg at cnio.es http://www.cnio.es