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...
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...
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...
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...
Tao, Thanks for the details. R command hclust takes in the distance matrix as parameter instead of standardized expression data, and I wonder how the centroid...
Hi, all. When I am reading 24 cel files of U133plus2 into dChip, I received some warning (red text) saying no MAS txt files, calculating present calls... Does...
Aiguo, Yes. You can also provide GCOS txt files for dchip to read: http://biosun1.harvard.edu/complab/dchip/open%20group.htm#txt Cheng ... From: aiguo li...
Dear Dr. Li, Thanks for your prompt response. Next question will be: Shall I do the normalization first or the model based expression first. As I understand,...
I've tried to load a sample information file and received a red message: No sample information found for the current array; probably wrong sample information...
Hi nice person :-) I want to run sample clustering, for this I need to filter my genes.. In the dialog box I apply criterias 1 and 2. I run it. It seems to be...
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