Hello, I have found that in the information file for the Rat UG34A chip, the entry for AA892041 (which is labeled as an EST in GenBank) was labeled as cyclic...
Jan Rodriguez
rodriguez@...
Jan 9, 2003 9:52 am
79
I think a better approach for analyzing your data is to export the MBEI and then test for differences in your samples using a t-test (or F-test if you have...
Jan, ... entry for AA892041 (which is labeled as an EST in GenBank) was labeled as cyclic nucelotide phosphodiesterase (Cam-PDE) while actually it seems to be ...
Hi, I have generated a list of genes that are differentially expressed between two animal models (with dChip expression values).Now we are going to publish it....
Christina, ... criteria? And the expression values with SE, of course. These are fine. You may mention the dChip version, the baseline array used for...
Hello, I am having difficulty using the combination of U133A+B information files. How does one combine both the HG_U133a_gene_info2 (including the protein and...
sasgharz <sasgharz@...>
sasgharz@...
Jan 14, 2003 7:47 pm
84
you need to use V1.3 to read new gene info file: http://biosun1.harvard.edu/complab/dchip/test.htm new gene info file for U133b may be created here: ...
Hi all, I think I have found a bug that is somehow involved with the export of expression data. Here is the problem. I analyzed some chips (import the chips,...
No, when I say PM/MM Data, I am referring to the icon by that name in the left panel in dChip that you can click to see the modeling information for individual...
Jim, the "Log transformation" may cause the problem. See note 12/9/02 here: http://biosun1.harvard.edu/complab/dchip/test.htm DCP files used to store log...
Cheng, I am using dChip 1.3 (a new build that you sent to me on 1/8/03) for the original analysis, and also to open the dcp file, so it should not be due to...
Jim, You are right. Please use the corrected version (you need to redo "model-based expression"): http://biosun1.harvard.edu/complab/dchip/test.htm Thank you...
Hi all Is anybody aware of a program that uses two-factor anova to analyze Affy data? The question I am trying to answer is whether any of the genes that show...
jdsandjd <josephd@...>
josephd@...
Jan 17, 2003 7:26 pm
92
Hi, Cheng: I happened to find this error in your 133A gene information file: probe set 203547_at should be CD4 antigen, and locus link is wrong too in your...
It's my mistake. Please use the new gene info file (after 12/14/02, produced by dChip annotator: http://biosun1.harvard.edu/complab/dchip/annotator.htm, so the...
When I perform hierarchical clustering, I notice that some, but not all, of the gene names appear in quotes (e.g. "gene"). Is there a way to get rid of the...
Cyrus, This might be due to that when Excel saves text files, it adds quotes to long strings. You may open the gene information file in a text editor (e.g. ...
I have run Affy chips on two groups of mouse frontal cortex tissue samples I am considering which is the best approach to analyze this experiment. Which are...
martapaterlini <marta...
martapaterlini@...
Feb 3, 2003 3:29 pm
99
I am a new user of DCHIP since this morning, and am struggling to analyse my data properly. If there is anyone in London, or failing that UK, who uses it...
Marta, You may try one of more of the software you mentioned and use the known changed genes to compare the results, or intersect the lists identified by...
I was wondering if running normalization to multiple arrays (control replicates) would be an improvement over the current method. I don't claim that I fully...
Jordan Sottosanto
jbso@...
Feb 7, 2003 6:55 pm
102
I do the same thing. I call it Super GEM. ... __________________________________________________ Do you Yahoo!? Yahoo! Mail Plus - Powerful. Affordable. Sign...
I think normalization tries to adjust overall bias of one array against another (or the average of all others), e.g. in terms of probe brightness in dChip. The...
I followed the dChip manual to install R, R-COM and dchip.R, but I still couldn't see "R command" button when I start dChip. Second question: in the image view...
... still couldn't see "R command" button when I start dChip. Please check "dchip.R" has the exact name, and you are using dChip Version 1.2+. ... few pink...
The Functional Genomics Facility Microarray Workshop May 12 through May 16, 2003 Biological Sciences Division, The University of Chicago The Functional...
Hello, I would be grateful for help on this: I would like to have the detection calls, with their p-values, into dChip (version 1.1). Is that possible? How do...
Christina, Please see here: http://biosun1.harvard.edu/complab/dchip/open%20group.htm#txt However p-values are not read and used by dChip. Cheng ... From:...
Hi all, I am comparing 2 cell lines (parental and mutant) and the second one is tetraploid with 4N DNA content instead of 2N. I wonder if the normalization ...
