I seem to hit a limit in the number of chips dchip will allow. Seems to be a hard coded constant around 400 chips (I currently have 411). Is there anyway to ...
Jai, You may use "Analysis/Compare samples/Combine comparisons" to intersect or union two or more "compare samples" gene list. Also the "compare on gene list"...
Hi Cheng, Thanks for the answer. The second options seems easier to me. I have one more question. Its realted to Hierarchial clustering. We here at our center...
Dear Cheng I am trying to set up the sample information file suitable for two way ANOVA (day vs group). I enclose the file. There are two replicates per group...
Hello, This email message is a notification to let you know that a file has been uploaded to the Files area of the dchip group. File : /Sample...
dchip@yahoogroups.com
Jun 14, 2005 10:40 pm
1142
Lawrence, Probably its’ due to that the groups are not balances? E.g. you don’t have two replicates for each Type X Days combination. I think you can try...
Dear Dr. Li Since Xba240 requires update to hg17 files I have tried to create a refGene file from refGene.txt and reefLink.txt. Since this new refGene file has...
Christian.Stratowa@...
Christian.Stratowa@...
Jun 17, 2005 6:12 am
1146
Christian, Thanks for the message and please update dChip to correct the problem ("Help/Latest Version"). Cheng ... From: dchip@yahoogroups.com...
How to use dChip to normalize non-affymetrix microarray data? I tried to use "Get External Data" to input it. Normalized it and selected "PM only" to do the...
Shengli, This looks OK to me. The “PM only” option does not make difference since you don’t have probe level data. Cheng ... From: dchip@yahoogroups.com...
Hi I have just recently started using dChip, and have a few questions. I am using the program to analyse Yeast 2 chips from affymetrix. I recieved, what turned...
Hi Astrid, I am not sure the difference between these two versions of dChip, but I think masking is the key here. Most probe sets in a mask file tend to get...
Astrid, It’s due to a change in the probe set mask file format this February: http://biosun1.harvard.edu/complab/dchip/open%20group.htm#probe_set_mask Please...
I did normalize... under analysis, of my six chips datasets. Then I can also see the graph from R program of normalized data compared to non -normalized data...
Jihua, What dchip version are you using? Please use the latest dChip here: http://biosun1.harvard.edu/~cli/dchip2004.exe And let me know how it goes. Cheng ......
Yes, I am using the latest version of the dchip ( June 20 ). And the error happens after I updated the cvs file from affymetrix website several days ago. ...
Hi Cheng, Thanks for your answer, I have tried your advise, but somehow it doesn't seem to solve the problem. Today I have discussed the problem with some...
Jihua, This is due to that the 6/21/05 Affy annotation CSV file contains very long entries for a probe set AFFX-MURINE_B2_at. Please use the latest dChip here:...
Dear Dr. Li: I downloaded dChipsnp from http://www.biostat.harvard.edu/complab/dchip/snp/ and try to use it look at 100k array data. I downloaded the library...
Hi, I'm having trouble making the genome info file for the 50K Xba array. I have tried following the instructions in the dChip manual but I don't get where I...
I'm trying to combine the two sub-arrays of 120K data: Xba set and Hind set. Following the instructions in the dChip manual, I obtain signal values using "Open...
