Dear All, I have a question about the Probe Data generated by using the "Export probe set" function. I was trying to gather the probe level data to investigate...
CM, Have you sorted the file by the Array column? It exports the probe data for all arrays. Cheng ... From: changqingma [mailto:changqingma@...] Sent:...
Thanks for replying my message. I actually found out the problem by sorting the file by the array column. After the sorting, for a probe set, all probes for a...
Hello, I was wondering if anyone has encountered this error message (below), and if so, what would you recommend to correct this situation? I am using dCHIP...
Dr. Cheng and others, We are working on LOH computation on SNP analysis (10K mapping arrays). When looking at the data in the Excel format, the genotype that...
Basically it is impossible. Strictly to say, the clusters basing on data are invalid. mshtkawazu <mshtkawazu@...> wrote: 1) I would like to know how to...
There are several methods to address support for a specific tree - bootstrapping using procedures implemented in PHYLIP; a Bayesian framework implemented in...
Hello, Where we can find explanation of different options for SNP array analysis? What is the meaning of "Compute signals separately" in Options-Model? ...
Yuri, These are options that we are developing and validating. Please ignore the options that appear in dChip but not explained in the manual – they are ...
Dear All, We have BAC array information and we want to correlate with gene expression. However, we are finding different problems. One is annotations, we have...
Pedro, If there is multiple chromosomal mapping for a probe set in genome info file, dChip will use the last one (row). This can lead to the difference you ...
When you mask redundant probe there is a way to do something like an average of the redundant probe sets in order to see an average expression for this gene, ...
Pedro, Only the first occurring probe set is kept in a gene list in this case. Cheng ... From: dchip@yahoogroups.com [mailto:dchip@yahoogroups.com]On Behalf Of...
Dr. Li. In the log2 transformed expression data, there are two cases that the 0 will appear as the signal intensity. 1) the original expression value is 1 and...
Aiguo, Exact 1) will rarely happen. If expression values is < 1, dChip will truncate it to 1 and then take log. Cheng ... From: dchip@yahoogroups.com...
Dear Dr. Li, shall we use dChip to analyze data from 100K SNPs (Affymetrix) now? For analysis of 100K, do we have to do anything different from the 10K...
Paula, Yes. please see this link: http://biosun1.harvard.edu/complab/dchip/snp.htm and use the latest dchip for 100K SNP array. Cheng ... From: Paula Kardon...
Dear Dr. Li, I've been trying unsuccessfully to analyze some 100K data and wondering if you have any suggestions. I'm using the dChip version from 4-15-2005 ...
Dear Dr. Li, Does dChip itself make SNP calls, or it just use the imported SNP calls from the GDAS? I've tried some data of 50k Xba240 chips. The SNP call %...
Irene, DChip only reads SNP calls from GDAS text files at "Open group". You may export the SNP calls read by dChip at "Tools/Export expression data", and ...
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....
