Hi, I am recently carried out some microarray analysis using 1.2 fold change as one of my comparison criteria. This gave me a reasonable working list approx...
i have carried out an affymetrix experiment using three biological replicates (the most we could afford). the experiment is looking at cell line response to...
Hello members, I am getting the following error when using the Analysis\Chromosome feature: Chromosome 1 length exceeds that of cytoband; are they from the...
David, What arrays are you working with? Make sure the genome info file and cytoband file are based the same UCSC genome assembly. Otherwise genes and SNPs (if...
This paper has a good example of using 3 replicates to find the gene candidate: Chemokine receptor CXCR4 downregulated by von Hippel-Lindau tumour suppressor...
Dear dChip users or Cheng, I'm using dChip to read Affy 100K data. Everything seems to be working fine except I'm missing the "chromosome" icon.... :-( Any...
Dear, untill now I only worked with GCOSand excel and now that I'm starting to use Dchip I have some questions. I uploaded cel files which I dowloaded from the...
Hello, I am trying to analyze 10K2.0 chips analyzed with GCOS 1.3 and GDAS 3.02. I receive the message "error: checkcell pos failed" all the time and I could ...
It’s computed as correlation coefficient using all the points in the scatterplot. Cheng ... From: dchip@yahoogroups.com [mailto:dchip@yahoogroups.com]On...
I ran into this problem the other day. You must do "Normalize" and "Model-based Expression" under the "Analysis" pulldown for a set of chips before exporting...
What type of analysis is conducted when looking for LOH in tumor only datasets. The manual says it ues the genotypes, but what are these geneotypes compared...
Dear Dr. Li, I'm trying to analyze the 10k 2.0 SNP Chip. Import of the CEL-files and the CDF-file has worked very well. But now, when I want to import the...
Dr Li: I have two points needed to be cleared. 1. Is the gene information file the same thing as genome information file for mapping10k XBa142 2.0? If not,...
Jacob, 1. See here to download genome info file: http://www.dchip.org/snp.htm 2. Yes the SNPID and AFFYID are the same. Cheng ... From: dchip@yahoogroups.com...
I loaded 102 samples. First I loaded the cell files via the Analysis/Open Group command. Then I normalized the arrays to the median intensity array. Then I...
I loaded 102 samples. First I loaded the cell files via the Analysis/Open Group command. Then I normalized the arrays to the median intensity array. Then I...
Hello! I am using dChip version release Apr 15 2005 and I encountered the following error when making the gene information file. {Make dChip information file ...
Please use the latest dChip here: http://www.dchip.org/manual.htm To correct the issue. Cheng ... From: dchip@yahoogroups.com [mailto:dchip@yahoogroups.com]On...
Hi, everybody I also got the similar errors (see below for detail), please suggest any. Thanks. Anyou Wang {Make dChip information file Reading Gene ontology...
Dr. Cheng, How does the program include measurement error in its accessment of group variability. Does it add it to the variance term when comparing two...
Alex, Please see page 5 of this link: http://www.dchip.org/li.pdf Cheng ... From: dchip@yahoogroups.com [mailto:dchip@yahoogroups.com]On Behalf Of Alex_Baras ...
Maria, This is not available in dchip. You can look into the SAM software. Cheng ... From: dchip@yahoogroups.com [mailto:dchip@yahoogroups.com]On Behalf Of...
I am wondering how to export data for a highlighting group with specific function, Like nucleic acid binding group, during cluster analysis. Thanks. Anyou...
Anyou, You can only export a clustering branch which may contain genes in other GO groups too. One alternative way is to use “Tools/Classify genes” to...
