Hi Kevin, Thanks for the observations. I agree and would recommend truncating them to 1 for downstream analysis. This may be done at "Analysis/MBEI" and then...
Chanchal, Unzip this link for mg_u74a.cdf: http://biosun1.harvard.edu/~cli/MG_U74A.zip I don't have other two. In my I understanding the v2 and v1 differences...
Hi Cheng, Thanks for the inputs. I am not an expert on microarray data but I read in an article that in terms of probe-sets there is only 80% overlap between...
Hi Martin, dChip uses a simplified MAS 4 algorithm to compute P/A calls: http://biosun1.harvard.edu/complab/dchip/open%20group.htm#txt If you have Affy call...
Hi Arrayprofile, For dchip inferred copy using median smoothing method, the smoothing window is 10 SNPs (5 on each side) surrounding each SNP. I don't think a...
Hi Zeshan, They are almost the same. Except for SNP array the A allele probe signal and B allele signals are summed for each PM or MM probe, to make AB, AA and...
Hi Michael, Exon array only has perfect match probes. Since dchip need mismatch probes to compute presence calls, they are all computed as absent. Cheng ... ...
Hi Hugues, You can supply a SNP list file at "Analysis/Chromosome/Gene or SNP list file", which is a text file and contains SNP probe set name on each row. ...
Hi Ellen, You can use "Tools/Array list file" to list tumor samples, but indicate normal samples in "sample info file" only. Then "Chromosome/Export SNP data" ...
Dear Cheng, dear dChip users, have you or has somebody already used the dChip software module CompareLinkage? I have been trying to work with it for several...
Hi Bart, Thanks for the question. In the latest dchip at "Options/Model" dialog, select "background subtraction" as "Mismatch probes" for PM/MM difference ...
Hi David, The ANOVA function is not special for exon data, so it just treats exon probe sets the same as expression probe sets and doesn't provide alternative ...
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 ¡°Analysis/Open group/Other info¡± containing these columns, then at the LOH view, use shift+down arrow to ...
Hi Christina, It¡¯s 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...
