Hi all, Can someone list the steps for using Illumina SNP data with dChip for CN/LOH? In particular, the call/intensity file: Raw or normalized data for...
Cheng The Illumina output gives the option for plotting allele specific Log2 ratios and thus allows us to find out whether there is mosaicism or mixture of...
Dear Dr Cheng, Manyt hanks for your previous help in getting me started with dChip. I am working with my data now but can not find amplifications. I have a...
Dear Dr Chrng, Many thanks for your previous answere. I need further clarification for this point: I did not specify any ploidy number for the samples. When I...
Dear Cheng, I have some question about the external data file. - Is it necessary to have a table's header? - Can dchip work with the file that don't have a...
Carina, They are probably founder or the first child (arbitrarily designated) of a family, so two alleles cannot be distinguished or assumed to always inherit ...
Hello, I'm new user for the dChip. While making information files, I am getting error message. I have cut and pasted the message below. Can anybody help me on...
Hi Cheng, When I want to view expression data along the chromosomes, I set the ploidy(numeric) column to "2" for my baseline samples in the sample info file,...
Hi Cheng, I was also wondering if it is possible to view the expression data along the chromosome with a range starting from less than zero? Because it seems...
Marc, You may use "Chromosome/Next data type" to toggle to log2 data view. ... set the baseline? Because when I export the LOH data, dChip gives values for the...
Hi, what does the error message "Vector sum is 0.000000 in MakeProb(); set to non-informative" in Linkage Analysis mean, is there a mistake in my predigree? ...
Hi Cheng, The recent update giving the option to export LOH on a per sample basis is very useful. Is there any way you could add a function to export LOH...
Carina, This is data overflow during computing and may mean the computed lod score at those SNPs are not reliable. You can reduce the pedigree size or do not ...
I have the same problem, the GO files are read, but when parsing the NetAffx CSV there is an error where a term is not found. I use the latest files from...
Dear Sir: Yes,I come across the similiar but much more serious problem. I use dChip to analysis my 500K SNP dchip genetyping results in a family with autosome...
Dear Cheng and other dChip users: I am trying to use dChip for copy number and I am unable to read the cel files. A worf file with a record of my run and a...
Richard Friedman
friedman@...
Apr 30, 2007 9:58 pm
2698
... David, I am using 10k chips. I have tried it with both "PM only" checked and unchecked. I believe that the log below shows that I am in the right working ...
Richard Friedman
friedman@...
May 1, 2007 2:37 pm
2699
Rich, This updated dchip (5/1) can also provide more error information to help determine what cdf file is needed: Http://biosun1.harvard.edu/~cli/dchip2006.exe...
The GO files i used was downloaded via the link from your page, but it works if i do not spesify the GO files. However, when I have the gene info file and try...
Hi, Dr. Li I would like to combine two different groups of dchip data which were separately normalized and model based-expression using normal control. I would...
Dear Cheng, I am quite new at running DChipSNP, and have a basic question; when I am trying to filter genes in preparation of gene clustering analysis (for now...
Corina, Since this is SNP array, probably you should not use P call % in filtering. Cheng ... From: dchip@yahoogroups.com [mailto:dchip@yahoogroups.com] On...
Dear Dchipper: I am using dchip to study a family pedigree using 10K SNP chip data. Here is my question. Each time I run the Merlin, it only analyze a specific...
Dear all, To better support the dChip software usage, we will switch to a forum to discuss dChip: http://dchip.forum5.com/. You can log into this forum and...
Hello everyone, I am pleased to announce that we are partnering with Bioinformatics.Org to do an online workshop on dChip using web conferencing technology. ...
Dear Dr. Li: Is it possible that you can given dChip a function to set an uneven range of CN in LOH? Such as 2-0.335~2+10. In this way we can encompass both...
Dr. Li, Which CDF file should I use for dChip copy number and LOh studies. BTW, Have you updated you dChip user manual recently? the latest on I found is 2005...
Hi, Can someone help me to analyze CN and LOH using dChip from SNP 5.0 array data. I need to know detail infoamtion regarding the the necessary files for...
