You may need to load a "Gene information file" at "Analysis/Open group/other information", and check "Tools/Optoins/Analysis/Additional gene information". Then...
Tongbin, You may use "Tools/Array list file" to separate replicate arrays, and then the sample clustering will be performed on averaged profiles. However...
Since Dchip data is already normalised what normalisation protocols (if any)are recomended for entry into GeneSpring, in order to center the data around 1. ...
Hello Cheng, We've been using dChip to analyze our Affymetrix chips for years, thank you!! However, we recently encountered few problems, hopefully we can get...
Pin, This looks strange. Do you mean you used only these 7 arrays as a group to do MBEI? Could you zip and email me your “array summary file” and the DCP ...
David, This is probably due to that the combined gene ontology and protein domain files have more than 1300 terms. I think your external data file is fine. You...
Hi, Cheng, I followed the steps listed in the website to install R and R connector, but when I done normalization, I can't view the R plot. What's wrong? ...
... When I click "Normalization plot", it will come out a small box and there is no message on it. The only thing I can do is close that box. But no plot show...
You may check the Affy facility lab where you hybridized the array. They usually have the MAS software installed on the PC of the GeneChip system, and the...
Mike, You may quit dChip and reinstall R-COM software to see if it works. R is usually working well and doesn’t need to be reinstalled. Cheng ... From:...
Mike Although not sure it was the same problem as I met, I did miss R after upgrade new version of dChip once, but I reinstall latest version of both R and...
Hello! Can anyone recommend an open source bootstrapping application for evaluating heirarchical clustering of GeneChip data? Are there any plans for a...
Hi, there, Do you know why the expression value exported from dchip does not have the same order as the gene information files, ie. the probe set are not in...
Dear Dr.Li, When I installed the R and open dchip, it shows the following information in R command option: Function call failed code:-2147221485 Text...
Wenbin, Probably we need to specify that the delimiter is tab. E.g. if dChip exported file looks like the following (no gene info file is used or gene info...
Mike, ... PM-only model is based on background-subtracted PM probe values. It gives positive-only expression values, but may suffer from having elevated ...
Actually the problem Wenbin is having is due to spaces in a field name. R does not distinguish between any type of whitespace (tabs, spaces, double spaces,...
You are right that Excel may add something to the file (e.g quotes around an entry with space). A dChip exported file is in tab-delimited format already ...
Casey, ... correction something that you always do or are there some small artifacts that you let go? Yes. The image correction corrects and overwrites the...
Yes. You need the CDF file for your custom array. If some parameters exceed dChip limit please let me know. Cheng ... From: Virtaneva, Kimmo (NIH/NIAID)...
Casey, ... They are computed using hyper-geometric distribution. More details here: http://biosun1.harvard.edu/complab/dchip/clustering.htm#gene_cluster ... ...
Hi all, I am currently writing up my D.Phil and am looking for publications where dChip has been used to analyse real data sets. I would be really grateful if...
Sanchita, In current dChip there is not such function. The invariant probe set is dynamically selected by comparing the baseline array and the array to be ...
