When I'm doing comparative analysis I get the message: "The file c:\Program Files\DCHIP v. 1.3\file name does not contain the comparison criteria usable with ...
Hi All, How can one filter genes based on intensity values (ex. 200 to 20000 fluoroscent units), i have something like 250 .CEL files! Eagerly waiting for your...
Dear Cheng, How can I have dChip analyze the CEL files directly and calculate data. The data directory contains the .CEL files from the arrays to be analyed. ...
Adriana, See http://biosun1.harvard.edu/complab/dchip/compare%20sample.htm#compare_criter ia Cheng ... From: adrianaprr [mailto:adrianaprr@...] Sent:...
Hi, For the genes I am interested I would like to look at the individual PM/MM data images. To do that I have to CEL image file--Probe together--View PM/MM...
Hi Cheng, After dChip reads in .CEL raw data, it checks the pairs for each probe set (gene), for each probe the relation (PM, MM) is calculated (is it...
Dear all, I'm using dchip sofware for the analysis of the Affy 10K SNP arrays. I run 5 matched samples of tumour/normal DNA from cutaneos lymphoma patients.I...
I downloaded "Mapping10K_Xba131 Annotations, CSV (2.2 MB, 10/12/04)" from Affymetrix website. When I tried to make information files, it is giving an error...
Molcyt, For SNP arrays, this is ideal since the samples in the same batch have comparable quality and variation level, so we can use information from normal...
I'm sorry, but I can't understand why I get the LOD score as right side curve in the loh data view and I can't see the inferred/raw loh. How can I adjust this?...
Hi, Just performed my dchip analysis, all diff expressed genes (127) are negative with just one showing posative expression (3 replicates of untreted/treated)....
Dear All, I am using dChip for my analysis for AtGen express microarray data. However I have tried hard to find files in cel format(I could only get the...
Arun, You can use the "Get external data" function without CEL files: http://biosun1.harvard.edu/complab/dchip/get%20external%20data.htm Cheng ... From: Arun...
Hello All I am a new user of dCHIP and am using a combination of custom and U133a probe sets. If I do hiearchical clustering on my excel file which is formated...
Dear users, I have affymetrix data that I have analyzed in genspring.I am interested in finding a receptor in this data.I have searched for the traceamine...
Hello all, Does anyone know of any problems using dChip on Windows XP - we have always used Windows 2000, but are getting some new machines. Thanks. -- David...
Hi! I know the linear discriminant analysis function requires R v.1.6, not the v1.7. All I can find is the latest, v2.0.1, and it doesn't seem to work with...
It works with R v 1.9.1, as well. ... -- David Carter London Regional Genomics Centre Robarts Research Institute, Room 4.01 PO Box 5015, 100 Perth Drive ...
I have Affy 10K SNP data from ten pairs of blood/tumor. I created a "sample information file" that lists the ploidy of all ten blood samples as "2". When I...
Eddie, You may set "Options/LOH parameter" > 100 to infer less changes. In this case the copy changes in normal is an estimated false positive rate. We are...
hello everyone,Can anybody recommend me a software that will extend microarray data analysis to the levels as following: 1. Chromosomal locolization and...
Hi All I have a few more questions as a new user of dCHIP 1) if one does for instance hiarchical clustering-is there a flat file created with the results that...
Hi All, Can dChip be used to find SNP's in Affy/Agilent microarrays data? Thanks, Hrishi __________________________________ Do you Yahoo!? The all-new My...
Hi I wish to see the list of genes mapped on the chromosomes, with the exact sites. working on an organism with a known genome Arabidopsis. I ran the basic...
Hi, using the current (obviously, not fitted) gene info file (downloaded from the Affy site), this is the feedback I get from DChip: {View data along...
