dchip at Yahoo! Groups

R interface

Cheng Li — Wed, 14 May 2008 22:37:17 GMT

Lene, This is the latest dChip: http://biosun1.harvard.edu/~cli/dchip.exe [V12/14/07+] Install R-COM (run

Multiple Testing Correction

jai — Tue, 13 May 2008 11:32:43 GMT

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

Installing R-COM interface

rasklene — Tue, 13 May 2008 08:34:59 GMT

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

Re: Help: making information files!!

Chia Chu — Fri, 09 May 2008 21:32:13 GMT

I see. Thank you for your quick response. -Chia --- On Fri, 5/9/08, Cheng Li wrote: From: Cheng Li Subject: RE:

Re: Help: making information files!!

Cheng Li — Fri, 09 May 2008 20:56:32 GMT

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:

Help: making information files!!

Jerry Chu — Fri, 09 May 2008 19:17:42 GMT

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

Re: dchipd gene info files- pig

David Carter — Tue, 06 May 2008 13:38:16 GMT

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

dchipd gene info files- pig

daughterofthedancingarabian — Mon, 05 May 2008 20:50:33 GMT

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.

Re: Individual array expression values disappeared

Cheng Li — Sat, 03 May 2008 00:34:16 GMT

Carol, You can try checking "Combine comparisons/output expression values". Cheng Li _____ From: dchip@yahoogroups.com [mailto:dchip@yahoogroups.com] On Behalf

Individual array expression values disappeared

mothersquid — Sat, 03 May 2008 00:17:31 GMT

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

Re: Help: Using dCHip for CN and LOH studies

Cheng Li — Fri, 02 May 2008 00:09:19 GMT

Please post dChip error messages. CL ... file, ... 5.0

Combine subarrays 500k

Antonio José Alberdi — Wed, 30 Apr 2008 15:37:40 GMT

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

Help: Using dCHip for CN and LOH studies

jishan561109 — Sun, 27 Apr 2008 17:21:26 GMT

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

SNP 5.0 CDF file

jishan561109 — Sat, 26 Apr 2008 23:41:19 GMT

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

Uniparental disomy

ccyen328.tw — Sat, 26 Apr 2008 14:23:31 GMT

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