I have a very similar problem to that described in question 105. I have followed the dChip manual to install R, R-COM and dchip.R, but I still couldn't see "R...
Causton, Helen
helen.causton@...
Apr 1, 2003 1:47 pm
163
Helen, Could you try attached dchip.R file? Cheng ... From: Causton, Helen [mailto:helen.causton@...] Sent: Tuesday, April 01, 2003 8:47 AM To:...
When doing a comparison anlaysis, the combine comparisons dialog box has a button to use a filtered gene list that is supposed to toggle between "use all...
Keith, Could you open the dchip.ini file (or group_name.ini file) in the same directory as dchip.exe, and change this line (or something like this): ...
Hi all, I wonder if there has been a modification of the similar profile function in the clustering menu since, when I check for symetric results, I dont get...
phguardiol@...
Apr 9, 2003 12:19 am
167
Philippe, Could you lower the correlation threshold to see if negatively correlated genes can be selected? Also I found the message output after this function...
Hello, anybody, As a new dChip user, I am just wondering how to filter some user’s defined functional groups like SOS, TFIIIA, Sp 1 related group and then...
Anyou, The latest gene info files contain the pathway information: http://biosun1.harvard.edu/complab/dchip/info_file.htm If you have one gene in mind, you can...
Hi, Cheng Thank you so much for your prompt reply. I have another associated question. If I have one gene a, how can I determine it to the location in its...
Somebody might ask this before. Is there a file some where out there containing the corresponding probe set IDs shared between the two chips? I have a gene...
Tao, Sorry for my premature suggestion. NetAffx right now doesn't have information on matched probe sets for the same organism. Please try this file: ...
Hi, I would like to compare four different experiments to a baseline chip to produce fold change data and then cluster this. I have logged all data to base 2...
Hi,Louisa I just started to use dChip a few day ago, but is it "OR" relationship (default) problem? If so, your result is ok and nothing wrong. Anyou Wang ... ...
Louisa, This looks right. For a gene, the baseline chip is not set to 0; instead, its expression value is standardized together with other samples: “Before...
Thanks, that makes sense now. Is there anyway of producing a clustergram with the baseline constant so as to show fold change values away from it?. Thanks...
Louisa, DChip doesn’t have this function; however you may first tranform your data into fold changes (e.g. in Excel, or tailor the dChip “Compare...
Hello, everybody Attached is error output I always meet when I try to export a group of genes using GO for E.Coli. Can you tell me what's wrong? Thanks. Anyou...
I got a longer name for gene ID, like /start=122092 /end=122856 /direction=+ /description=transcriptional regulator for pyruvate dehydrogenase complex ? Thanks...
Anyou, Could you try the latest version here: http://biosun1.harvard.edu/complab/dchip/test.htm (see note 4/7/03) If not working can you email me your input...
Hello, Cheng Thank you reply. I already used the new version. I input all genes like ... Read gene information for 7290 genes Analyzing gene annotational...
Anyou, Thanks for letting me know the problem. Please try the correction version: http://biosun1.harvard.edu/complab/dchip/dchip.1.3.exe Cheng ... From: Anyou...
Cheng YES, it is working!!!. Thanks a lot. but the gene name still incuded start/end position and orientation +/-, something look like " /start=2500010...
Anyou, You may use the previous version of Ecoli gene info file here: http://biosun1.harvard.edu/complab/dchip/info_file.htm which has more concise gene names;...
Cheng
Thanks again.
Attached you will find data of one group I exported by
using different version, but I could not find out which
version I used because I...
Mirzo It is working for my E.Coli. data. I thought I tried human133A before, it also worked very well. Based on different GO terms, different groups with P...
