Hi, I want to do Affy 100K SNP chip analysis. I want to combine the 50K Hind and Xba data and analyze them together. I did follow the instructions under the ...
Dear Dr. Li and dear users, I'm running dchip to infer copy number of 13 matched normal/tumour samples with Affy 10k. I'm using the PM/MM difference model and...
There is a “Quantile normalization” option in “Tools/Options/Model”, which is similar to what RMA uses. Cheng Li http://biosun1.harvard.edu/~cli/ ... ...
Mainul and Sandeep, Could you try this updated version to see if it corrects the problem: http://biosun1.harvard.edu/~cli/dchip2006.exe If needed, when opening...
I have loaded my .cdf file and have several CEL files in the directory I am refering to, yet I keep getting the following error "Found no files of this...
Make sure you check "Open group/Filetype: CEL", and specify "Mouse430_2.cdf" as the cdf file for this dataset. You can copy the dchip output messages to here...
Dr Li: Is there a way to import a copy number tables (first col: SNPID, then each column is the copy numbers from each sample) into dchip and make use of the...
Dear Cheng I have used a different method to infer LOH, and am trying to read this back into dChip. The uninferred LOH file was used for the external analysis...
Hi , I'm new to Dchip . I would like to get some data files to start learning it. I'm not able to get the data files. ( i'm missing some files or the other ) ...
The data set I am using is actually GSE2926 which uses the U74A chip, so I have the correct cdf and downloaded the correct CEL files. Someone mentioned that...
You may try winrar to unzip it. Make sure the final unzipped CEL file has *.cel extension and can be opened by text editor to see probe signals. Unzip this...
This is because not all the SNPs on the array have mapped genome positions. What's the error message? Make sure the "external data file" has first column as...
Dear user, this is the first time that I'm using dchip software. I failed to upload my results in the software by following the web manual guide. There is any...
Hello Dr. Li, I am starting with dChipSNP and am testing the Affy 100K tumor data set and the HapMap data set. I can get through converting both of the .cdf ...
Are you using the latest dchip? Can you copy the dchip output messages from the start of "Open group"? Cheng Li http://biosun1.harvard.edu/~cli/ ... From:...
Yes, I've tried the latest 2005 and 2006. Here are the messages from dChipSNP2006 (2005 gives me the same messages): Welcome to dChip 2006 (DNA-Chip...
You should use a cdf file with the original name of such as "Mapping50K_Xba240.CDF" instead of "Xba240.cdf", so dchip can recognize it's a SNP array. Cheng Li ...
Hi Cheng, This is Wenhong Fan at Fred Hutchinson. Thank you for being a reviewer in NIH grant review committee. We submitted a U19 proposal on GVHD and got a...
Hi Wenhong, Thanks for the note. Make sure you save in text format (for gene info file) or CSV format (for affy annotation CSV files) after you copy the...
My suggestion is don't rely only on the inferred copy numbers - they can contain false positive or negatives. Rather, use key "I" to check the raw copy...
Hi all, How do I download dchip. Thanks in advance. ... Brings words and photos together (easily) with PhotoMail - it's free and works with Yahoo! Mail....
The masking function only works at the clustering step. You may first cluster these genes, and then use "Clustering/Export branch data" (first select all the...
You can register in dchip yahoo group and then go to "Links" to find the previous versions of dchip. The difference is probably caused by some settings. You...
