Tony, Please try this copy of R 1.6. It appears to be able to install. http://biosun1.harvard.edu/complab/dchip/rw1062.exe Cheng ... From: French, Anthony...
Jing, Probably it's due to the SNP ordering when exporting TXT from GDAS. Be sure to keep the original ordering of the SNPs (as in CDF file) at the exporting ...
Jin, Copying the messages from the dchip analysis view (Use "Analysis/Copy") and then paste in the email is fine. For slow model-based computation, you can try...
Charles, Yes more sample info can be added: http://biosun1.harvard.edu/complab/dchip/open%20group.htm#sample_info For tumor cell %, probably you want to add...
Dear Dr. Cheng, Sorry to bother you. My problem is too easy to ask you, but, I have tried and studied your papers which impressed me very much. I have done the...
Chang, See this page for CDF files: http://www.dchip.org/snp.htm Also you cannot directly use Affy CSV file as genome information. Instead, download them here:...
I read some paper saying lots of Affymetrix probe set sequeces don't match their coresponding mRNA sequence? If so, the gene expresion level based on probe...
Dear Dr. Li, Thank you for your previous help. I have used dChip to analysis array data today. The DCF file is installed, there are two DCFs for 100k set, but,...
Even the probe sequences do correspond to the gene sequences, the calculated gene _expression levels are absolutely not accurate. 1. Mei Xu. Theoretical...
Chang, You may use the method here to combine the two sub arrays: http://biosun1.harvard.edu/complab/dchip/snp.htm#combine Here is format of sample info file: ...
Dear Dr. Li, I am using dChip in analyzing some Affy 100K SNP chips. Here are some questions I cannot find answers in the manaul. 1. When comparing 20...
Irene, 1. One run is ok. Use sample info file to specify normal samples. 2. What you are doing is fine. The score in the copy number analysis is the copy...
Theresa, Please use the updated dChip here: http://www.dchip.org/manual.htm to read the genotype text files from GEO. I also added related note in the manual: ...
Hi Cheng, We have been analyzing 100K SNP array data in dCHIP as individual 50K sub-arrays but have had no success loading the combined text file from...
Dear Dr Li: Is the sample info file for the NCI60 (GSE2520) in paper http://www.nature.com/nature/journal/v436/n7047/full/nature03664.html available anywhere...
dear cheng, i am still at the early stages of working out how to use Dchip on my 100K SNP data. For the moment I am analysing the Xba and Hind chips ...
Dear Dr. Li, Sorry to bother you again. When I use the normalization function of dChip, I choice one subject as my baseline array. Then the dChip will accsee...
Chang, Normalization only needs to be done once, using a particular baseline array. You may use a different array as baseline and then compute expression...
Greetings - Recently we started working with a different class of specimens for arrays. I wanted to specify a text file sample list for dChip to read in files...
Natalie, You may try some data here: http://biosun1.harvard.edu/complab/dchip/snp.htm#dataset A baseline array is best to be visually clean with even...
Hi Paul and other 100K users, Have any of you had success in combining the Hind and Xba chips yet? Many Thanks Natalie ... 50K ... row- ... version) ... close....
Dear Cheng, The analyses we are doing using 100K SNP arrays doesnt involve any normal controls or paired sample data, only tumor samples. We may have access to...
Hi Natalie, ... could give when analysing tumor samples alone? Do you think the inferred LOH (from the HMM) is reliable enough to identify small regions of...
Dear Cheng, sorry - this is probably quite straightforward, but I cant find any details on how to change the size of the type/gender/ploidy information in the...
Natalie, You may first uncheck “Chromosome/Proportional distance”, and then use shift+up or shift+down arrow and left or right arrow. Cheng ... From:...
I have just started working with a 50k SNP chip to analyze genome amplifications and LOH events. I am having trouble locating the 50k gene info file into...
Martin, SNP info file is a new file type for filtering SNPs. You don’t have to specify it so you can go to downstream analysis. I will try to post the SNP...
Hello All, My apologies for putting this question on dChip list but am hoping that other microarray users will try to answer my questions regarding SAM. I am...
