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...
Dear Dr Li: I can visualize and analyze each 250k array set but I don't arrive to combine 250k Nsp and Sty arrays. Please, could you to indicate me how to...
Hello, I recently replaced my dCHIP2005 with the latest download from the website. My compare_result files with the old version would show probeset expression...
Carol, You can try checking "Combine comparisons/output expression values". Cheng Li _____ From: dchip@yahoogroups.com [mailto:dchip@yahoogroups.com] On Behalf...
Hello, Can you tell me if gene info files are available for the pig? I've tried looking for them on Affymetrix's site to no avail. Thanks! Marsha C....
Hello Marsha, You can make the gene info file within dChip using the Affy porcine annotations .csv. I made them 2 years ago with no problem. Look under ...
Hi, I want to use dchip to analyze some e_coli_2 arrays but the program shuts down due to error every time when I try to generate information files from...
Chia, dChip has not been tested on making gene info file for this array. You may manually copy and paste columns to make a file. Unzip this file for a format: ...
To Dr. Li, I have recently installed dChip to analyze some array data. In addition I have installed the program R to be able to do some LDA. Installing the...
Hi Cheng, Can dCHIP perform Multiple Testing Correction e.g Benjamini and Hochberg, Bonferroni etc. I could not find them in Compare samples. Just wondering if...
Lene, This is the latest dChip: http://biosun1.harvard.edu/~cli/dchip.exe [V12/14/07+] <http://cran.r-project.org/contrib/extra/dcom/> Install R-COM (run...
Dear all, We now have a new dChip user group at here: http://groups.google.com/group/dchip-software <http://groups.google.com/group/dchip-software> Also,...
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