Dear all. I am trying to analyze my mapping 10K SNP data (5 tumor cell lines plus a standard cell line) using dChip. In array list file I created a list file...
Aiguo, You have to have paired normal and tumor samples from the same individual to do LOH analysis in dChip (normal first, then tumor). Is your "standard" ...
Dear Dr. Li, I did tried to use the standard sample first in array list, then the tumor cell line followed. However, it created a chromosome picture with all...
Aiguo, Since you don't have paired normal samples for each tumor, you may look into signal analysis instead: X Zhao, C Li, JG Paez, K Chin, PA Janne, TH Chen,...
Dear All, I am new kid on the microarray block. Could you please tell me exact location where I can get the CDF file for Arabidopsis 25k chip. I want to run...
I haven't been able to download dChip.exe from the link below for the past several days. Is there a new site? http://biosun1.harvard.edu/~cli/dchip.exe Thanks,...
I asked the same question yesterday and Cheng Li gave me the following download link : http://biosun1.harvard.edu/~cli/dchip2004.exe Julie AUBERT ... I haven't...
Hi Cheng, Thanks for taking care of the mailing list and addressing all the questions. This takes a lot of your time. Here I have another question: I have a...
Jamie, This is fine. FDR method is a type of multiple comparison adjustment: http://128.32.135.2/~sandrine/Docs/Papers/Test_spe.pdf You may also try SAM...
Cheng, I really like your cluster analysis platform. For maximum versatility I'd like to suggest that you make it possible to specify different types of...
Hi I need to know exactly what the option of Trimmed signal parameter in the newest version of dCHIP does. the option is in the settings tab under chromosome....
Hi I am new to this software.... while normalizing, I wish to view the scatter plot, and I get the following message: "Couldn't start R, Please refer to DChip...
Michali, Check out: http://www.biostat.harvard.edu/complab/dchip/interface_r.htm I have insatlled R from: http://cran.us.r-project.org/bin/windows/base/ ...
Hi, I have been trying to make the gene iformation files work, but so far no success. I am working with the C. elegans chips and have downloaded csv files from...
Hello Cheng, I am using R affy library. In this I am using expresso(rma, invariantset, pmonly, liwong) to get the exprssion profile of 22 experiments. However...
After normalizing and analyzing a group of arrays using the PM-only model, I used Export Probe Set to examine the probe-level information. My question is...
Hess_ann, Yes. The PM and MM probes are first normalized against the baseline array, then the background is computed using the normalized probe values and ...
i am on my travels and need to download another copy of dhip. How do you do this I have forgotten. I have been to the website but there is not an option to...
Download the latest version from here: http://biosun1.harvard.edu/~cli/dchip2004.exe ... -- David Carter London Regional Genomics Centre Robarts Research...
I am getting an error message that says no matching mas text file. The names of the genes are not linked to the probe sets. I have the cdf file and gene...
Hi everyone Can someone explain to me the new ANOVA filtering function? Here's the precise problem. I have three experimental groups, each with biological (not...
Lawrence, Yes you can use the function to filter genes that differ in one or more groups. Specify the group label in the sample info file. However, the ...
Dear all, I would like to analyse 2 of my gene chip experiments with D-chip. One set of targets has been hybridized on Affy (mouse) Moe430A chips and another...
Dear Cheng Would a valid approach for three experimental groups therefore be to 1. Filter to find genes present in (e.g. at least one) array. 2. Filter...
Hi, Cheng and all: 2 questions (I'm using dchip2004.exe): 1) When I de-select the "standardize rows" in the clustering option, how come the color of all the...
Tao, 1. This is because the displaying range is set at "Tools/Optoins/Clustering" to be [-3, 3], and standardization brings value to roughly this range. If you...
Lawrence, I feel that (1) followed by ANOVA is ok, without further pair-wise comparison. You can view the top gene list by “Clustering” and tell the change...
