Jan, Resampling is a good idea to test the robustness of clustering and classification. You may paste and run the following R code in R to do resampling: #...
Hi, We have been trying to export clustering images from the latest d-chip 1.3 as .emf files, however we have been unable to open them in Illustrator 10...
diyoo2
liebert@...
Mar 7, 2003 3:31 pm
131
The only option I have found is to use the 'Picture and Fax viewer' that comes with windows XP. This program allows you to zoom in without the text becoming...
Toby, Could you try the following and let me know how it goes? "To convert dChip exported EMF files into EPS format, one may try the following by using Adobe...
Hi. We are working with experiments with replicates. When we run comparison analysis, the results are different if we make the Experiment and baseline groups...
Mikko, Please see this note: "Here is one comment about the degree of freedom of the t-test. If both groups have one sample (each is the pooled result of N...
... the ... Illustrator ... a PDF ... editing, ... may use ... extension to ... cannot ... OK, that seems to have worked, I installed Acrobat, inserted the...
diyoo2
liebert@...
Mar 17, 2003 6:47 pm
136
Does anybody have a good way to compare U95A vs U95Av2 chips? I have a program that does this ... Determine Input Cel file type (U95A or U95Av2) IF (U95A) { ...
Jamie, Please unzip this file: http://biosun1.harvard.edu/~cli/dchip_manual.zip I will make it available from dChip website soon. Cheng ... From: jamie zhou...
Thanks a lot, Cheng! I appreciate it. Jamie ... From: Cheng Li To: dchip@yahoogroups.com Sent: Tuesday, March 25, 2003 11:22 PM Subject: RE: [dchip] pdf manual...
Cheng, Just out of curiosity, in this manul, PM only model is kind of ignored. I havn't really follow on this lately, but does this mean something or just I am...
Thanks for the URL to the PM only analysis at http://biosun1.harvard.edu/complab/dchip/pm%20only.htm . The text there says "When a cross-hybridizing non-target...
Richard, ... stronger to the MM probe? I know the theory is that it's supposed to determine non-specific binding; but what if the reality is that it's picking...
Wen, What do you see at “PM/MM data view”? Does the animation show different intensities values for a spike-in gene in different samples? Could you export...
Hi Cheng, I can see the difference in PM/MM view (see the screenshot in the attached file) There are two attached files: One is exported expression values...
Hi, Wen: I'm not sure why you only used the data from 4 chips (as shown in the picture in your word file)? There are way more chips on the download center....
Tao, The a-d chips do have various concentrations for the spike-in genes. For example, 1708_at has concentration 1024, 0, 0.25 and 0.5. Wen, I can reproduce...
You're right, Cheng! I missed the "99" in the chips' names. Do you think the sample size would affect the normalization or MBEI calculation? ...Tao Cheng Li...
... calculation? Yes. See "Add new arrays" section in this link: http://biosun1.harvard.edu/complab/dchip/prepare%20data.htm Usually the more arrays the...
Hi Cheng, I finally figured out what is going on. I have tried "ignore existing ..." at every step, but it doesn't seem to solve the problem. I have to hit...
Wen, Could you email me the old and the new data file list so I can check? Usually if you put all files in a directory and specify a data directory may be a...
Dear Cheng, I have a question regarding replicates, as far as I understood, I can indicate the samples as replicates only in case when they are experimental...
Mirzo, In your case you don't need to pool replicates (see below for more details); if you have two replicates for each of the 6 samples you may pool...
Dear Dr Li and others, I am sorry to bother you with this, but I would really appreciate an answer. Is it better for me to go from 1.1 version to 1.2 version...
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