Hi Eric, Please use this updated version: Http://biosun1.harvard.edu/~cli/dchip2006.exe Which has an array limit of 2000. Thanks for the suggestion. Cheng Li ...
PhD Student Position in Statistics in Switzerland on Bayesian Methods for Integrated Genomics IOSI (Oncology Institute in Bellinzona) and IDSIA (Artificial ...
Dear Dr. Cheng Li, I'm using dchip to analyze an Affymetrix SNP array. Therefore I'm working with dchip as told in your manual in the chapter "dChip: SNP array...
Hi Christina, You will need to do normalization and modeling for copy number analysis: http://biosun1.harvard.edu/complab/dchip/copy.htm#copy_number but not...
Hi, I read from the manual that dCHIP can perform LOH analysis of the tumor samples without the matched references, but cite to a reference that is not...
I am using dChip 2006 (DNA-Chip Analyzer), Build date: Feb 16 2006 I find that I get a different(lesser) number of genes when I do a compare samples analysis....
Hi, Dr. Li. I have a set of 200 chips from 2 affymetrix platforms: some chips from U133A and U133B and some from Plus2. Is there a way that I can normalize the...
Hi Aiguo, They cannot be loaded into the same dchip group. However, they may be combined row-wise (A and B array) first and then combined with plus2 array ...
Hi Farhad, The different is most likely due to the new default option is checked at “Options/Model/Truncate negative PM/MM differences to 0”. As a result...
hello all, when looking at the clustering of snp data, eg 50k chips, is there a way to rearrange the dendrogram like we do when examining expressiond data with...
Hi I keep on getting an error message after about 30seconds of having dchip site open. 'Microsoft Internet will have to close'. I dont have this with any other...
Natalie, Thanks for the message. This should be due to our web server problem. Hopefully it will be ok today. Cheng Li http://biosun1.harvard.edu/~cli/ ... ...
Dear Sir: I try to use the most update dChip 2006 to analyze 10 K SNP array data (Affymetrix). But it cannot read the CDF file (Mapping10K_Xba142.CDF), which I...
What’s the error message? Cheng Li http://biosun1.harvard.edu/~cli/ ... From: dchip@yahoogroups.com [mailto:dchip@yahoogroups.com] On Behalf Of ccyen328.tw ...
Dear teacher : When I use dChip sofeware to get theta and phi (model based analysis expression index computation) .I find that the phi of dChip output does...
Dear Dr. Li, Sorry to bother you again with nearly the same question, but do I have to do normalization and model-based expression when I'm performing a...
Hi Christina, Normalization and MBEI are not needed for linkage analysis, unless you want to try SNP based copy analysis to see if your samples have deletions...
Michelle, Most likely its because that only the phis that are not probe outliers are restricted to have sum square of J (the number of probes that are...
Chueh-Chuan, You may follow the similar ways as 100K data, although you may need to prepare you own reference genotype file. Since in 10K array SNPs are...
Dear Cheng, Thanks a lot - you're the best online help I ever got! But nevertheless I have to bother you again with some questions about some basics (sorry,...
April 17th, 2006 Dear dChip users and developers, To continue to maintain and develop the dChip software, we are preparing a grant application titled...
Hi, I have used dChip 2005 built Dec 11 2005 and dChip 2006 built April 10 2006. Now when I try to load my 55 samples the program just crashes. Sometimes I get...
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Hello Anouk, I'm sure the importing worked fine. dChip is just letting you know that it was a binary file and that as there was no MAS file, it is generating ...
Dear Dr Li: We have data of 100K (mapping50Kxba240) from bunch of tumor cell lines, but no normal reference samples. There are 100K normal SNP cell line...
