Dear Cheng Li, Thanks for your rapid reply. I have tried this file that you gave the link to but unfortunately it gives the same errors. I have also tried to...
Hi Cheng, I went through both versions of dCHIP and I found that "Truncate negative PM/MM difference to 0" is a new feature. But since you have incorporated...
Could you copy the dchip error message? Cheng Li http://biosun1.harvard.edu/~cli/ ... From: dchip@yahoogroups.com [mailto:dchip@yahoogroups.com] On Behalf Of ...
There is no need to have gene expression for "Analysis/Genome" function, the gene list is fine. You may use "Tools/Export expression data" to get expression...
Hi, I am doing copy number analysis on 100K affymetrix SNP array data using dCHIP. I need to compare the intensity difference between the Hind and Xba array....
There is not such a function. But you may redo "Analysis/Normalize" (check "ignore existing normalized data in dcp file") and see the normalized median ...
Hi Cheng Yes I still see a difference between HMM and median smoothing if I run them consecutively on the same data, while changing nothing else. If I switch...
Hi!! I am analyzing some SNP arrays and wanted to know if there is another option to generate the .txt file with the genotype information appart from opening...
I wonder if there is a batch mode in GTPYE that can do this for many arrays. Cheng Li http://biosun1.harvard.edu/~cli/ ... From: dchip@yahoogroups.com...
Hi Cheng, thanks for your answer, actually if you open more than one .chp file in GTYPE, the data of different chips will be added as more columns to the same...
Hi Cheng Li, This is the error message I get when trying to select the information file for the exon arrays. Kind Regards, Justine ... -- *Justine Peeters* ...
You should specify the pgf instead of the cdf file. Download and unzip the library <http://www.affymetrix.com/support/technical/byproduct.affx?product=huexon-s...
Hi Cheng, With help from a friend, we generated a new gene info file (.xls) that includes the GO terms for pombe genes. I saved it as a tab- delimited .txt...
Could you send me the file so I can check? Cheng Li http://biosun1.harvard.edu/~cli/ ... From: dchip@yahoogroups.com [mailto:dchip@yahoogroups.com] On Behalf...
The main purpose of this option is to make all-positive expression values under the PM/MM difference model, similar to truncating the PM - background to be...
Hi, I’ve run dchip2006 for copy number changes with 10K samples. Everything worked and the results is seems to be difficult to analyze based on variation in...
Dear Cheng, I have specified this file when I open the group but unfortunately I do not get the option to look at the information in analysis/chromosome. I ...
Hi,Cheng I am wondering how to use correlation filtering.When I select absolut correlation or rank correlation,it gives the same results as neither is...
You need to select a gene or gene cluster in the clustering figure, and then use correlation filtering. Cheng Li http://biosun1.harvard.edu/~cli/ ... From:...
Dear Dr Li: A quick question. For dchip version 2006, users can calculate the SNP copy numbers for two alleles separately. I noticed that the plot for the...
Dear Cheng, We are interested in gene set enrichment analysis with custom gene sets. Could we use Dchip for this application for hundreds or thousands of...
Hi Jacob, PLASQ is not in dChip and dChip uses a different algorithm so it may not give the same results. But I think it$B!G(Bs a good sign if different...
I am working on copy number analysis using dChip software. I had hard time to read the manu and couldn't make it work. Can someone write steps in more detail...
Hi, Dr. Li. Would you please tell me how I can convert the Affy probesets for U133-X3P chip to the ones for HG-U133A.1.3? I have a gene list consisting of ...
You may get such information here: https://www.affymetrix.com/support/technical/comparison_spreadsheets.affx Cheng Li http://biosun1.harvard.edu/~cli/ ... ...
Hi, I am going to create a genome informatioon file for 100K SNP array. My CSV file is Mapping100K_annot.CSV and I wonder which GO file I should use ann where...
