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 ...
Philippe, Do you hybridize DNA on the chip? If you have controlled so the amount of final hybridized DNA (or RNA) is the same, the arrays should be at a...
Hello, I just wonder how you others do when you analyze you data, do you log transform the values when you make the MBEI values? I have not done that, and I...
Christina, I almost always log transform my data. There are two main reasons to do this. First, the un-transformed values have a strong right skew and almost...
Christina, Jim, Cheng, A nice discussion why to log transform the data is on Terry Speed's site: http://stat-www.berkeley.edu/users/terry/zarray/Html/log.html ...
... This idea is adopted by methods such as Robust Multichip Average: http://nar.oupjournals.org/cgi/content/full/31/4/e15 Cheng ... From: Klacansky, Igor...
Hi, When considering the results of combining comparisons is it necessary to perform any statistical tests? Presumably some of the genes that overlap between...
diyoo2 <liebert@...>
liebert@...
Feb 24, 2003 6:08 pm
118
A rough way is to use binomial or hypergeometric distributions; e.g. if gene list 1 selects 100 genes out of 10k, and the gene list 2 has 200 genes out of 10k,...
Hello, I have been working with dChip for over two months now, and would like to suggest a feature. Let me describe the background of my suggestions. I work...
Jan Rodriguez
rodriguez@...
Feb 26, 2003 1:42 pm
123
Hello, If anybody has the time to explain what exactly a the residual curve in grid 1,3 is, I would be grateful. My comprehension on this is not 100%. Thank...
Christina, There are three 'curves' in grid 1,3. The blue curve is the actual intensity values for each probe. The red curve is the fitted value for each probe...
Hi all, I d like to analysis with the "genome function" 4000 genes but it seems that it is too many for dChip ! how can I overcome this ? Thanks Philippe...
Philippe, Do you refer to the "Analysis/Genome" function: http://biosun1.harvard.edu/complab/dchip/map%20chromosome.htm In fact all the genes can be specified...
Jan, Resampling is a good idea to test the robustness of clustering and classification. You may paste and run the following R code in R to do resampling: #...
Hi, We have been trying to export clustering images from the latest d-chip 1.3 as .emf files, however we have been unable to open them in Illustrator 10...
