Dear Cheng I am trying to analyze data from the new rat 230 2.0 array. To do this presumably I need to combine the CSV files for 230A and 230B. I tried to...
Lawrence, You can first download the two files with names like: HG-U133?_annot.csv ? is A or B. then go to “Start/programs/command prompt” and go to the...
Anyou, You can follow the steps here: http://biosun1.harvard.edu/complab/dchip/gene_info_file.htm#make_info_file and let me know how it goes and error...
Hi, Dr. Li Thanks a lot, but the error was still the same (attached for detail). Is it possible that something wrong in lastest csv file? DrosGenome1...
Hi, Dr. Li Thank you so much for fixing it, but after downloaded, it could not be opened in my MS-XP system in my computer (DELL INSPIRON 8600, 1920*1200). The...
Hi, i am having a problem with Dchip: when I load the samples in the "open group" window" and i normalize and do the model-based analysis the final results...
One thing i liked when MAS5 came out is that i didn`t have to deal with negative affymetrix exprewssion values. It makes vaery hard the interpretation in terms...
Andrew, You can select “Analysis/model-based expression/options/model/pm-only model” in dchip to obtain positive only expression values. See more details...
Robert, You point to a useful resource. The best match files contain the information how the probe sets in the two array types of the same organism relate to ...
Hi everybody! I have been having trouble reading in DAT files from the HG-U133A 2 chips when using the appropriate Affymetrix download Library files (*.cdf). ...
"By default an array with median overall intensity is chosen as the baseline array against which other arrays are normalized at probe intensity level" Is the...
Andrew, If the default array has obvious image artifacts, or has low P call % or high array outlier %, it’s good to redo normalization using a different ...
Dear all, I want to convert some DCP files generated around January 2001 back to CEL files, and wonder if you have and could share with me a dChip 2001...
Hi, Dr. Cheng Li. I sent an e-mail to you last week (please see below) hoping to get your help. I some time have trouble with my e-mail box. May be you never...
Hi, I am new to dCHIP, here is what i want to do: i have a list of genes for which i want probe level data (PM,MM),i read in CEL and CDF files and when i try...
Zhong, We did reply but probably the email didn't come through your mailbox. We will be happy to look at your data and I will ask my colleague, Ming Lin, to ...
Hi, I was trying to read in a .DAT file via dChip and export it to a .CEL file. No matter whether I check the option 'Export probe set name, probe paire order ...
Wei, Dchip-exported CEL files contains less information than authentic cel files. You may present the first 100 lines of its content to affy package authors to...
Hi, Cheng. Thank you for your positive response. I am gald that you have arranged Ming Lin to lead the collaboration. There is something need to be discussed....
Dear Dr. Li, Thanks a lot for your quick response. I looked at the CEL file generated by dCHIP and the authentic CEL file from MAS for the same chip, yes,...
Hello everybody! I am wondering, if it is possible to cluster genes only that have met my filtering criteria. Since I am using HG133 plus 2 chips with human ...
Hi Kevin, I haven't used dChip on the HG133 plus 2 arrays, but for other GeneChips, I just select: Analysis -> Hierarchical clustering -> click the gene list...
Hi David! Thank you very much for the help .... it worked... at least in part ....the output (all red) however seems a little suspicious ... but that's fine...
Ok that worked out fine .... my next problem is, that I would like to re-organize the branches clustered ... as they are now, the samples of the same group of...
Hi Kevin, Selecting Cluster samples in the clustering window should do it. Replicates will cluster together. ... -- David Carter Research Technician London...
Sven, You may right click a branch to switch its two children, so the visualization changes. But the interpretation of the clustering result remains the same. ...
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