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...
Dear Cheng, Thank you. The clustering tool definitely helps visualise the results. However, having obtained a list by ANOVA, in order to draw statistical ...
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...
trying to create gene info file. As directed, I have downloaded CSV file from affymetrix, and the 3 GO files. CSV in its format and the 3 GO files txt format. ...
Hi, I am just a beginner but I am running into the same problem as Crystal. I think that Yu's suggestion would also work for me, but when I try to access...
Hi All, Where can i download MG-U74-A VERSION 1 CDF file? Thanks, Hrishi _______________________________ Do you Yahoo!? Declare Yourself - Register online to...
Hao, Letting them use dchip to view images may be easy. E.g. you copy all the dcp files of a PI in to c:\anyname directory, and copy dchip.exe and cdf file ...
Hi Cheng, It appears clustering genes gives more significant gene groups (under the cluster icon in the left pane) than classifying genes in the "Tools" menu....
Dear Dr.Cheng, Can dCHIP be used for Agilent data? Thanks, Hrishi __________________________________ Do you Yahoo!? New and Improved Yahoo! Mail - 100MB free...
