Dr. Li I have some 10K SNP array data that need to be analysed. Which version of dChip I should use? And where can I find the correct genome information...
Hi Anton, You steps are fine. But you need to do “Analysis/Filter genes” to use less than 2000 genes for clustering. I don’t recommend removing unknown...
Hi Qi, You should use the latest dchip: Http://biosun1.harvard.edu/~cli/dchip2006.exe And “11k_snp_genome_info_hg15_asian.xls” in hg15.zip. Cheng Li ...
Hi, Previously I have normalized and fitted the expression model to 30 samples. I have just received a further 30 samples and wish to use my previously...
Hi all, Please find attached a call for an open PhD position. We would be glad if anyone with good dChip experience would apply for this position. Please feel...
Dr. Li I downloaded dchip2006.exe to my c drive, but gor following error when trying to run it: "The dynamic link library gdiplus.dll count not be found in the...
Locate this file on your PC or download it from the net, and place it in the folder where the .exe is located. ... -- David Carter London Regional Genomics...
Hi Jane, HMM length is mainly a practical consideration since for 500K array one chromosome can contain 50K SNPs, but the SNPs far apart don't provide much ...
Hi Martin, You can refit using the previous 30 samples but generate a PSI file: http://biosun1.harvard.edu/complab/dchip/model-based%20expression.htm#psi_fi le...
Hi Cheng, I am back to trying to get the GO terms into the gene info file. I still get the same errors and my friend and I were troubleshooting and found that...
Hi Jun, Yes 1300 is hard-coded limit in dChip. You may select the most frequent 1200 or so GO terms and put them in the dchip gene info file. Cheng Li ...
Probably not. You better use Bioconductor to do this. Or you can use dChip Tools/Export probe set to get PM and MM values but log transform when you do...
Dear Charlotte, First thank you very much for the strong support letter, many suggestions in which will be very useful for future development. When you do not...
When I try to build an information file, I run into the: "NumTerm==MaxTerm at category Gene Ontology..." I use the April 29 2006 version (tried also the...
Hi I want to download gene information file for rat230_2 array.I am not able to find in affymetrix can any one help me? Please send me the link . Regards ...
Hello, I am using: dChip 2006 (DNA-Chip Analyzer), Build date: Apr 29 2006 I am trying to analyze snp chip example data linked to from the dchip site: ...
Hello- I recall reading someplace that the newest release of dChip will only run on Win2000... is this correct, or will it run on XP too? we are buying a...
Hi all, I was wondering if you could help me out with this import problem I'm having. I have a set of Hind240 CEL files and a CDF file which I downloaded from...
These are early access 50k snp arrays, not release version. So should use cdf file for early access. cheng ... From: "serandor" <natemiller@...> To:...
We recently started unchecking "Load Probe Data in Memory" when doing MBEI when loading new chip data into dChip (we use Affy 50k Xba SNP chips). We've noticed...
... Hello, I am only one step ahead of you (I just asked a similar question). You should also have 5 corresponding output files from affy's software (probably...
Hi, I am new with dchip. Trying the do some linkage analysis with 10K Affy arrays and having some problems. Everything was fine until using the chromosome tab...
Hi, I have performed my standard array analysis using dchip, but now would like to use the expression profiles generated to look at the genetic networks...
Hello, I am using: dChip 2006 (DNA-Chip Analyzer), Build date: Apr 29 2006 After succefully opening (loading) one single snp experiment, I am able to look at...
Dear Cheng, could you explain in more detail about the 'Options/Average Heterozygosity rate' function and how this would decrease the small (erroneous)regions...
I think GenMAPP will be a good software to look at pathways. PathwayAssist also looks nice: http://www.ariadnegenomics.com/products/pathway/ Cheng Li ... From:...
Hi John, The latest dchip is compiled on XP so should run on both XP and 2000. Cheng ... From: dchip@yahoogroups.com [mailto:dchip@yahoogroups.com] On Behalf...
Hi all, I am trying to make a common probe set files between HuGeneFL and HG- U133_plus_2 array. As instructed by the manual, I download and unzip the...
