Hi, I have successfully gotten external data from XLS file. Would I be able to view the array image, PM/MM data, and model-based expression indexes with this...
Susan, Log transformation is determined by the "Analysis/Open group/Options/Log transform expression values" option and is effective in this "Open group" ...
Hi all, I am relatively new to DCHIP and have a query that I was hoping someone might answer for me. In compare samples when I select for genes differentially...
Gino, This is due to the way dChip computes means by considering measurement error attached with expression values. Please see note 5/21/03 here for more ...
Igor, Thanks for the file. Please see below for my comments. ... different culltures (dif RNA) and done in two different times (2 wt 2 mut, with a difference...
Sanchita, All permutations giving large number of genes are the same comparison as the original one (1,2 vs 3,4), so you don’t need to worry about them. I...
Hi, I'm trying to export some Dchip images and would like to select and color multiple sample branches. Using ctrl+click only allows me to select and color up...
Hi, I am working on a project dealing with Affymetrix Genechip image processing. I was wondring if there is any free genechip image processing libraries...
Walid, DAT file is in TIFF format. See page 18 of this file: http://biosun1.harvard.edu/~cli/GATC%20software%20specifications.pdf Cheng ... From: wskamoun...
Hi, I was wondering if there is any document that describes all the image processing methodologies implmented in dChip. I mean addressing (Gridding),...
The gridding is done in the same way as MAS (converting DAT to CEL): http://biosun1.harvard.edu/~cli/Expression%20analysis%20algorithm%20tutorial .pdf (page 6)...
Hi, Thanks for your quick answer but I still dont find the gridding algorithm in the PDF file. They directly jump to intensity averaging assuming that the...
Hello, I'm using dchip 1.2 and having difficulty in getting the Gene Ontology annotations. I have saved them as text files. I don't have the "Tools/Make...
Hi, Does anyone know how MAS5 calculate the P/A calls. Do they report genes with absent calls some specified value or report the original intensity for those...
Hello, MAS5 bases the P/A calls on the discrimination score which is = (PM-MM)/(PM+MM). This is calculated for all the probe pairs in the probe set and is...
Sachin, Some recent gene info files require V1.3: http://biosun1.harvard.edu/complab/dchip/test.htm Let me know if you observe problems in using it. Cheng ... ...
Has anyone seen a difference when looking at comparative analyses performed on dChip build 1.3 (March 03) vs. 1.3 (test 7-10-03)? I have conducted the same...
Hi, I have questions about opening CEL and CDF files. I got both CEL and CDF files from one of our collaborate labs and tried to used dchip to analyze it....
All you need are the cel and cdf files. Are you getting some sort of error? If you say what error you get, it will be easier to figure out what the problem is....
Hi all, Say, if I want to import a list consisting of Affymetrix ID into dChip and export the corresponding expression data or classify the imported list, is...
