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new dChip user group and onsite course Dear all, We now have a new dChip user group at here: http://groups.google.com/group/dchip-software Also,
Cheng Li
Dec 31, 2008
R interface Lene, This is the latest dChip: http://biosun1.harvard.edu/~cli/dchip.exe [V12/14/07+] Install R-COM (run
Cheng Li
May 14, 2008
Multiple Testing Correction Hi Cheng, Can dCHIP perform Multiple Testing Correction e.g Benjamini and Hochberg, Bonferroni etc. I could not find them in Compare samples. Just wondering if
May 13, 2008
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Installing R-COM interface To Dr. Li, I have recently installed dChip to analyze some array data. In addition I have installed the program R to be able to do some LDA. Installing the
May 13, 2008
Re: Help: making information files!! I see. Thank you for your quick response. -Chia --- On Fri, 5/9/08, Cheng Li wrote: From: Cheng Li Subject: RE:
Chia Chu
May 9, 2008
Re: Help: making information files!! Chia, dChip has not been tested on making gene info file for this array. You may manually copy and paste columns to make a file. Unzip this file for a format:
Cheng Li
May 9, 2008
Help: making information files!! Hi, I want to use dchip to analyze some e_coli_2 arrays but the program shuts down due to error every time when I try to generate information files from
Jerry Chu
May 9, 2008
Re: dchipd gene info files- pig Hello Marsha, You can make the gene info file within dChip using the Affy porcine annotations .csv. I made them 2 years ago with no problem. Look under
David Carter
May 6, 2008
dchipd gene info files- pig Hello, Can you tell me if gene info files are available for the pig? I've tried looking for them on Affymetrix's site to no avail. Thanks! Marsha C.
May 5, 2008
Re: Individual array expression values disappeared Carol, You can try checking "Combine comparisons/output expression values". Cheng Li _____ From: dchip@yahoogroups.com [mailto:dchip@yahoogroups.com] On Behalf
Cheng Li
May 2, 2008
Individual array expression values disappeared Hello, I recently replaced my dCHIP2005 with the latest download from the website. My compare_result files with the old version would show probeset expression
May 2, 2008
Re: Help: Using dCHip for CN and LOH studies Please post dChip error messages. CL ... file, ... 5.0
Cheng Li
May 1, 2008
Combine subarrays 500k Dear Dr Li: I can visualize and analyze each 250k array set but I don't arrive to combine 250k Nsp and Sty arrays. Please, could you to indicate me how to
Antonio José Alberdi
Apr 30, 2008
Help: Using dCHip for CN and LOH studies Hi, Can someone help me to analyze CN and LOH using dChip from SNP 5.0 array data. I need to know detail infoamtion regarding the the necessary files for
Apr 27, 2008
SNP 5.0 CDF file Dr. Li, Which CDF file should I use for dChip copy number and LOh studies. BTW, Have you updated you dChip user manual recently? the latest on I found is 2005
Apr 26, 2008
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Uniparental disomy Dear Dr. Li: Is it possible that you can given dChip a function to set an uneven range of CN in LOH? Such as 2-0.335~2+10. In this way we can encompass both
Apr 26, 2008
Online workshop on dChip Hello everyone, I am pleased to announce that we are partnering with Bioinformatics.Org to do an online workshop on dChip using web conferencing technology.
Cheng Li
Apr 24, 2008
dChip Yahoo group will be switched to a dChip forum Dear all, To better support the dChip software usage, we will switch to a forum to discuss dChip: http://dchip.forum5.com/. You can log into this forum and
    Cheng Li
    May 23, 2007
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    Dchip merlin linkage study---- Chromosome Dear Dchipper: I am using dchip to study a family pedigree using 10K SNP chip data. Here is my question. Each time I run the Merlin, it only analyze a specific
    Zhang, Jacob
    May 14, 2007
    Re: Filtering Genes Corina, Since this is SNP array, probably you should not use P call % in filtering. Cheng ... From: dchip@yahoogroups.com [mailto:dchip@yahoogroups.com] On
    Cheng Li
    May 3, 2007
    Filtering Genes Dear Cheng, I am quite new at running DChipSNP, and have a basic question; when I am trying to filter genes in preparation of gene clustering analysis (for now
    Corina Shtir
    May 3, 2007
    Re: Help!! Martin, You can check if the external data file is saved in txt format. dChip manual has links to CDF files:
    Cheng Li
    May 1, 2007
    How to combine data together ? Hi, Dr. Li I would like to combine two different groups of dchip data which were separately normalized and model based-expression using normal control. I would
    mengmin liu
    May 1, 2007
    Re: Help!! The GO files i used was downloaded via the link from your page, but it works if i do not spesify the GO files. However, when I have the gene info file and try
    Martin Strand
    May 1, 2007
    Re: Unable to read cel files. Rich, This updated dchip (5/1) can also provide more error information to help determine what cdf file is needed: Http://biosun1.harvard.edu/~cli/dchip2006.exe
    Cheng Li
    May 1, 2007
    Re: Unable to read cel files. ... David, I am using 10k chips. I have tried it with both "PM only" checked and unchecked. I believe that the log below shows that I am in the right working
    Richard Friedman
    May 1, 2007
    Unable to read cel files. Dear Cheng and other dChip users: I am trying to use dChip for copy number and I am unable to read the cel files. A worf file with a record of my run and a
      Richard Friedman
      Apr 30, 2007
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      Re: haplotype color Dear Sir: Yes,I come across the similiar but much more serious problem. I use dChip to analysis my 500K SNP dchip genetyping results in a family with autosome
      Apr 28, 2007
      Re: Help!! This may be a bug to handle the latest GO files. You may try these recent gene info files here instead:
      Cheng Li
      Apr 27, 2007
      Re: Help!! I have the same problem, the GO files are read, but when parsing the NetAffx CSV there is an error where a term is not found. I use the latest files from
      Apr 27, 2007
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