Aiguo, It's not required to use the same array as before for normalization. It's better to analyze all arrays in one group and normalize to the same baseline ...
Hi, When I use genome view the mapping stops before finishing all the chromosomes. Also, are there any reccommended machine specs for dCHIP1.3+? thanks jason...
Jason, Can you paste the dchip error messages? A general Windows system is ok for dchip 1.3. Cheng ... From: sjorges2002 [mailto:sjorges2002@...] Sent:...
Cheng, Sorry to bother I fed the wrong annotation file. Is there any way to change the max stretch limit? I have a windows system. I'd like to know what kind...
You can use the method here to make one: http://biosun1.harvard.edu/complab/dchip/gene_info_file.htm Cheng ... From: jgmcnoyola [mailto:jgmcnoyola@...] ...
Hi all, I am attempting to load some of Affy's reference data for the human 100k Xba/HindIII chip I into dChip. I have the CEL, CHP, and EXP files, as well as...
Ah, so what is the maximum SNP count that dChip can handle at once? And is there an ETA for even an alpha or beta version of dChip SNP that can handle 50K or...
Hello dChip group, I am trying to use the Chromosome function and am getting some error messages. Can anyone point out what I might be doing wrong? {View data...
David, The refGene.txt and refLink.txt files downloaded form UCSC <http://hgdownload.cse.ucsc.edu/downloads.html> need to be combined by Microsoft Access to...
hi! Cheng: I have multiple samples from 4 tissue types. I think it was recommended to do the MBEI per tissue type separately. Could you tell me how to compare...
hi! Cheng: I think I got the answer, I found this from Dchip Manual: "This requires putting different tissues in different dChip groups (e.g. create a...
No errors now - thank you. ... -- David Carter London Regional Genomics Centre Robarts Research Institute, Room 4.01 PO Box 5015, 100 Perth Drive London,...
I would like to see the normalized values for an external data set. After I "Get External Data", I chose "Normalize" to perform the normalization. Then I...
hi! cheng: My understanding of the situation is as follows: 1. if there are very different tissues, then put them to separate group and do normalization...
Hello dChip users: I am new to the software program and am in need of some assistance. We are currently trying to analyze our Map10K SNP array data with dCHIP,...
Hi, Does anyone have a prebuilt Drosophila 2.0 chip Genome information file they could send me? I thought one could be built fairly quickly with the make...
Hi guys, Attached please see a hierarchical cluster of some of my data obtained by dChip analysis. Now, the cluster itself, I can comprehend perfectly, while...
Hello, all. I have one data set of 90 chips and would like to get the expression values for both PM only model and PM-MM model. Should I do all three process...
Aiguo, You only need to do model-based expression twice. Normalization is the same for both options. Cheng ... From: aiguo li [mailto:li9212001@...] ...
Hi, I am presently using dChip to analyze Affy 10K SNP (early access) chip data. I am attempting to do some clustering on my samples. I have been able to...
Thanks Cheng. Is there an efficient way,using dChip, to take the probe sets that are generated in the cluster analysis and trace them back to their location...
Analysing the same array-results with dChip and CCNT give different results. A deletion is easily confirmed but a very good visible duplication in CCNT is...
http://biosun1.harvard.edu/~cli/dchip2004.exe ... -- David Carter London Regional Genomics Centre Robarts Research Institute, Room 4.01 PO Box 5015, 100 Perth...
