Jonathan, "Inferred LOH call threshold" is used only when exporting LOH data: http://biosun1.harvard.edu/complab/dchip/snp.htm#export_data For display it's...
Charles, Thanks for the suggestion. Please use this 9/22 version: Http://biosun1.harvard.edu/~cli/dchip2006.exe And check "Chromosome/Export snp data/Output...
Shaila, I don't. You may use this mapping file between the two arrays: http://biosun1.harvard.edu/~cli/SNP%20match%20100K%20EA%20vs.%20release.txt and the...
Celso, Thanks for the message. You may try this 9/29 version: Http://biosun1.harvard.edu/~cli/dchip2006.exe Which uses at most 300 probe pairs for a probe set....
Hi Libi, 1) There is no automated way. However if you check "Open group/Perform normalization afterwards", multiple steps will be run at once. 2) Affy right...
Hi Rich, You need to use a sample info file at ˇ°Analysis/Open group/Other infoˇ± containing these columns, then at the LOH view, use shift+down arrow to ...
Hi Christina, ItˇŻs used for faster computation, but may lead to false peaks. So if time allows and pedigree is small, you can uncheck this option. Cheng ...
Hi, I am using dchip to analyze the Novartis GeneAtlas dataset for the mouse. I imported the data using the Novartis CEL files. When I look at clustering...
cheng hi, i found the "analysis/analysis of viation" icon was gray most of the time in the dchip version of 2006/5 .it only can work when the cluster was done,...
Hello- I am using dchip version 2006(2). I have noticed a problem in the output files when exporting SNP Presence call data. It appears that SNPs with a...
Hi John, This is caused by dchip representing chromosome positions as real value (4 bytes float) instead of integers. I think the rounding error should be ...
Hi, I am currently trying to analyze some cel files associated with HT_HG-U133A Arrays. I see in posting 2293 that someone did so successfully with Build...
Hi, I'm working with de HG U133 Plus 2.0, and I wolud like to know if you could help me because i don't know how to create a correct gene list or where obtain...
Hi Laura, Only NetAffx Analysis Center can annotate correctly the Affymetrix probe sets. There is no publicly-available database for generating all genes...
Hi Xin, Probably the r2 version of the pgf files have a somewhat different format. Right now I may not work on this issue, but you can try Affy’s EXACT tool ...
Hi Cheng Li, I am using the Oct. 10 2006 build of dChip and I see in the chromosome view for mapping data that there is a column for SNP call. How can I ...
David, If you use "Tools/Export expression" to export SNP signal data, then use "Get external data" to read back (uncheck "SNP array"), you can use "Compare ...
Hi Cheng, Just a quick question/problem regarding exporting of SNP data. I am interested in exporting regions with a specific threshold (significance curve...
Hi Cheng, Related to my previous question about exporting significant regions, I noticed this function doesn't work at all for raw CN. Is this correct?? This...
Hi Peter, I have seen similar situation. Hom in normal and Het in tumor often indicate genotyping errors, and it occurs simultaneously with intervening changes...
Dear Dr Li, I normalized a dataset of about 400 U133 plus2 chips and now need to normalize additional 210 chips. I may need to integrate this 210 chip dataset...
Aiguo, Dchip can handle 2000 arrays as hard limit. It’s depending on memory practically. You can uncheck “Open group/options/load probe data in memory” ...
Dr. Lr, That is helpful and thank you so much, Aiguo Ehen, I have 3G memory on my machine. It was ok for me to normalize 360 chips, but when it comes to 550...
