Xinmin, Please try the dChip test version: http://biosun1.harvard.edu/complab/dchip/test.htm and follow the descriptions in note 10/12/02 for this purpose. I...
Dear group, dear Cheng, I recently analyzed the Affymetrix latin square experiment with dchip. This experiment consists of 59 HG_U95A (version 1) arrays with...
Hi Reinhard, Thanks very much for pointing out this. ItĄŻs known to me that dChip 1.1 sometimes doesnĄŻt convert old CDF.BIN or DCP files correctly, and...
Hi all, Has anybody had weird results with MG_U74Av2 chips using dChip v1.1? Here's the story; Today I was analyzing 12 of these mouse chips, and after...
When I 'open a group', I run into troubles, and I hope somebody can tell me how to get it right. I have been using Dchip without any problems for a number of...
b1wertheim
b1wertheim@...
Oct 23, 2002 2:06 pm
6
Hi Jim, Thanks for the message. Here are some thoughts: 1. MG_U74Av2 has chip names on the top originally (in scrambled format), probably not so after...
LocusLink doesn't have GeneOnotology terms for Rat. One possible approach is to map Rat genes to human genes (eg. HG_U95A arrays, see mapping here: ...
Hi Cheng, Thanks for your response. I still have a couple of questions though... As you say, if you can read the lettering at the top of the CEL image, the...
... files). After re-reading the files, my data was of course not normalized or modeled. I don't remember this ever happening before. Is dChip supposed to ...
Hi, Cheng apparently, the use of v 1.2 has resolved the problem. Thanks for your help Reinhard ... 1.1 ... this ... make sure ... group/Other ... group to ... ...
Hi, To my experience, it might be that your computer ran out of memory. Trying to reboot your computer would probably help. But eventually you will need a...
Another comment: When you switch to a different version of dChip to analyze an old data set, after reading in the files, check the array image. Sometimes you...
Hi, Cheng: Do you mean the MBEI from two different runs should be EXACTLY the same or just in the ball park? I can't image they are exactly the same based on...
I only know this one. ... You can ignore this. I think you have created a array list file before for another project, but somehow dChip still remember it even...
they should be exactly the same. all the algorithms are deterministic. even when random numbers are used when pooling expression values of replicates, this is...
Yes you should try tuning MAS5 software to give better P/A calls (I think this tuning is a feature of MAS5). Sinc Affy calls are validated using their internal...
I am also among the few who are interested in the abosolute P/A calls. The MAS5.0 algorithm is supposed to be better than the MAS4.0 algorithm used in Dchip to...
dchip only accepts "probe set mask file": http://biosun1.harvard.edu/complab/dchip/open%20group.htm#probe_set_mask and relies on a model for probe selection: ...
Hi, Cheng: Imagine I take some DCP files from expriment #1 and experiment #2 which have been normalized and calculated for MBEI within each experiment along...
The answer is yes. Since DCP files contain both unnormalized and normalized CEL values, and normalization always uses the unnormalized CEL values. cheng ... ...
It started to happen to me recently. The sample names right under the tree branches are very small (in dChip 1.0 and 1.1), no matter how long I changed the...
The Right key can enlarge the sample names, and The Control+down key will spare more vertical space for the sample names. Let me know if there is problem. ...
Joni, You may try to delete the description column and then save as TXT file (or not export this column into TXT files) . A row (for hg-u133a probe set ...
Hi, I have whole bunch of questions. Is it possible to combine 133A and 133B data in dChip? Can I do it just by combining the gene information files and the...
Tao, ... Yes. You may follow descriptions here: http://biosun1.harvard.edu/complab/dchip/combine%20chip.htm#sub_chip ... MBEI outputs? Yes you may combine the...
you may use "View/Export image" to export the images into BMP or JPG format and then import files into Word or Powerpoint to print the picture. (v1.2...
... These are the PSI of one gene, 16 probes in a set, using PM only model in Dchip. I thought the sum of square of PSI should be the same number of probe(16)....
... iteration ? Yes. This phi is a probe outlier since it has large value (phi^2 > sum(phi^2) * 0.9) and probably it also the large standard error attached....
... numerical-statistical evaluation (normalization, evaluation of mean/median/sd, fitting, clustering)? Outlier expression value refers to the "array outlier"...
