hi During a recent discussion in my lab the following question was raised... can dChip be used to analyse other chip types that are not Affymatrix? Such as...
Dear Cheng I am trying to use the latest NetAffy CSV file for Rat 230A chip. I download and unzip it, and it comes as a .CSV file. When I juse Open Group>Other...
Dear Cheng I am now trying to convert the Rat230A CSV file using the MAKE INFORMATION option. I get the following error message: {Make dChip information file ...
Dear Dr. Chen, I found that dCHIP only masks out redundant genes if they have different probe_set name but same locus link. However, dCHIP doesn't mask out...
Hi Can anyone tell me what the figure in the upper bound of fold change column means in the compare samples output file ? Also Some of the probe sets have a...
Dear colleagues I have performed two different analyses using dChip in order to discover differentially regulated genes between two cell types taken from each...
Yan, You may supply a gene information file for this external data file, and put artificial LocusLink ID for your probes in this file. Cheng ... From:...
Dear Cheng, I am trying to filter out all the probe sets that are called ABSENT in all arrays and generate a list of probe sets to carry out my analysis with....
I got a series of CEL files yesterday. Each file was about 3Mb and was not readable by dChip program. I guess those are the new binary type files. But when I...
Minkyuoh, You may zip and send me one CEL file so I can check. Using DAT files is also ok. Cheng ... From: minkyuoh [mailto:minkyuoh@...] Sent: Thursday,...
Lawrence, Could you copy and paste the data line of this gene in the compare result files of the two options so I can check? Usually paired t-test has more...
hi! All: I wonder if I have a set of affy results, but they belongs to different categories, should I using dCHIP to put them in different groups? then apply...
Hi,all, I want to export the filtered gene lists, but I cannot find the "Tools/Export data/Expression value" in the software as the manual said. Is it the...
Dear All: I have a data set that contains about 100 chips, about 7 different categories since the sample from different tissue. I made data file list and...
Hao, ... the first step? Yes. The DCP files contain unnormalized and normalized probe values, as well as model-based expression values. ... group that contains...
hi! Cheng: Thanks for your reply, I am confused about the sequence I should apply the analysis, my understanding: 1. make different data location files for...
Hao, If you decide to analyze all tissues together, you can put them in one directory and open them in a single group. Following the sequence in manual or...
Hi, I'm using dChip 1.3 to analyze Affy 10K SNP chips for LOH. I'm having trouble getting my LOH display to allow me to view the gene names and SNP IDs. These...
Sean, You may use Control + Right key or Right key to adjust the width. 11K genome info file is based on Affy annotation files, which also has African American...
Dear All: I hate to ask it here but I can't find an answer to my question even after reading the dCHIP manual. The situation is like this, I have 150 chip for...
We are trying to use Dchip to analyze the new Affy chip (MG0430 2.0), and I am getting the error message "number of probe sets exceeds limit". Does the most...
Please see this link for the latest dChip: http://biosun1.harvard.edu/~cli/dchip.exe cheng ... From: Victoria Perreau [mailto:vperreau@...] Sent: Thursday,...
Hao, ... try to combine them together for ArrayTools analysis? Yes. ... them into one group and do analysis after what I already did? You can first combine all...
Hi, Cheng Could you explain the first question a little bit more. I previously thought when we did normailization and MEBI with d-Chip, no further need for ...
