Dear Dr. Li, how will we analyze 100K data using dChip? I mean, do we have to analyze 50K Xba and 50K HindIII array data sets seperately or can we combine them...
I was interested in checking out this article but don't have access to this journal through University of Washington. Could you please forward the pdf to me? ...
I downloaded the annotation csv file for the u133A chip. I am trying to compile the genome information file. This is the message I get... What should I do? ...
Please update to the latest dchip to handle the problem. Cheng ... From: dchip@yahoogroups.com [mailto:dchip@yahoogroups.com]On Behalf Of michmintz Sent:...
I have a subset of genes that I want to calculate the correlation between...different combinations of ligand/receptor pairs. does anyone know if there is a...
Sara, You may export the expression data of these genes, and read in the R software and use the cor() command. Or you can do hierarchical clustering in dchip...
Excel will do this with the correl function... ... From: dchip@yahoogroups.com [mailto:dchip@yahoogroups.com]On Behalf Of stajhashimi Sent: Tuesday, May 10,...
Lisa Lai <lisaannlai@...> wrote: I was interested in checking out this article but don't have access to this journal through University of Washington....
You may email the author to request a pdf copy; the email address can be found here: http://www.worldscinet.com/jbcb/03/0302/S0219720005001193.html Cheng ... ...
According to this paper the probe set data form a fixed pattern. But we have observed misbehaved probes: within a probe set only one or couple of probes vary...
Dear Dr. Li I've been using dChip to analyze commercial Affy arrays, but I moved now to custom-made Affy chips. When reading the "custom-made" CDF file (as I ...
Hello, I have a problem reading data files specified in a data file list. I put cel files names in a text file with full path, but ask dChip to read dcp files,...
Dear new friends, I am a new comer in this e-group, a new face in this field and would like to ask some question in my experiment to all of expert in this...
Hi Dr Li, I realized that the software and the genome inforamtion sheet for Xba240 have been updated. Thank your group for all the work to make dChip better. I...
Irene, 1. -1 means missing here. The physical distance is used to approximate genetic distance (1Mb~=1cM). 2. The genome info files on website is based on...
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...
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