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...
816
Cheng Li
l7501
Aug 4, 2004 7:44 pm
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"; ...
817
aiguo li
li9212001
Aug 6, 2004 1:51 am
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...
818
Cheng Li
l7501
Aug 6, 2004 4:21 pm
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,...
820
Arun Rawat
r_microarray
Aug 8, 2004 6:21 pm
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...
821
aiguo li
li9212001
Aug 9, 2004 4:37 pm
I assume that you are using arabidopsis expression array from affy. You should be able to find the cdf file in the following URL: ...
824
jim_rathman
Aug 9, 2004 10:16 pm
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,...
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Julie Aubert
julie_aubert
Aug 10, 2004 6:55 am
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...
828
jim_rathman
Aug 14, 2004 2:59 pm
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...
829
Cheng Li
l7501
Aug 17, 2004 10:31 pm
Jim, You may toggle “Options/Clustering/standardize rows” to standardize or not standardize genes. The reason for standardize genes is for centroid...
830
clare_whelan2003
clare_whelan...
Aug 18, 2004 7:43 am
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....
831
mikijafe
Aug 19, 2004 1:05 pm
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...
832
David Carter
dcarter442000
Aug 19, 2004 1:22 pm
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/ ...
833
mikijafe
Aug 19, 2004 1:32 pm
Thanx - I'll try... ... the ... the ... <http://us.ard.yahoo.com/SIG=129gvle3r/M=298184.5285298.6392945.30011 ...
834
suvivartiainen
Aug 24, 2004 10:59 am
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...
835
Arun Rawat
r_microarray
Aug 28, 2004 11:15 pm
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...
836
hess_ann
Sep 2, 2004 7:51 pm
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...
837
Cheng Li
l7501
Sep 2, 2004 7:53 pm
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 ...
838
crystal1tips
Sep 6, 2004 12:59 pm
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...
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David Carter
dcarter442000
Sep 6, 2004 11:02 pm
Download the latest version from here: http://biosun1.harvard.edu/~cli/dchip2004.exe ... -- David Carter London Regional Genomics Centre Robarts Research...
840
crystal1tips
Sep 7, 2004 1:25 pm
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...
843
thfpeters
Sep 9, 2004 5:15 pm
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...
845
Shi, Tao
shidaxia
Sep 9, 2004 7:22 pm
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...
846
Cheng Li
l7501
Sep 9, 2004 7:58 pm
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...
849
Cheng Li
l7501
Sep 10, 2004 6:34 pm
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...
850
aiguo li
li9212001
Sep 10, 2004 8:52 pm
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...
851
Cheng Li
l7501
Sep 10, 2004 8:58 pm
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...
852
aiguo li
li9212001
Sep 10, 2004 9:19 pm
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,...
853
galit
galitis2004
Sep 12, 2004 10:26 am
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...
854
mikijafe
Sep 12, 2004 10:37 am
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...
