Hi, Cheng, I have a question for combining subchips for SNP study. Currently I normalizae the Nsp and Sty chip seperately to the chip with median probe...
hi, I have the same problem before, but I figured out that if you check the box "load the data in memory" when you load the data, you will have those image...
Lin, You don’t need additional normalization. This is because the raw copy number is obtained for each SNP by dividing the mean of normal samples at this...
Hi Cheng, When I run copy number analysis, I got the following warning message: Reading genome information file 'H:\dChip\supplemental files\mapping 100k\100k...
Thanks, Cheng, you are right. But is it necessary that the two baselines the same normal sample ? Or I would prefer the baselines to have the MPI evenif they...
Hi Cheng, I noticed that dChip makes a background correction of the probe set intensities. Can you explain how this correction is done ? How the background is...
Hi again, I read somewhere that this correction was done after normalisation but I found it as well before normalisation when I export the probeset values. ...
Hi Cheng, I am trying to export chromosome regions with copy number analysis. In the dChip manual as below, it is said I need to "specify "Standardize...
Hi Philippe, This link contains details for background calculation: http://biosun1.harvard.edu/complab/dchip/model-based%20expression.htm#pm_onl y It’s...
Hi Cheng, I output the raw and infered copy numbers for my 100k SNP arrays. I found that the first 82594 rows (or snps) are ok, filled with copy numbers for...
Dear Cheng, Using the 'Compare samples' function I can do t-tests between two groups of samples but I was wondering if I can do any non-parametric test in...
Hi, Cheng, I tried to make a common information file for MOE430_2 and MOE430A arrays followed the instructions on the website, but the program crashed, could...
Dear Cheng (and other Dchippers) I am analysing 250K and 500K SNP arrays - looking at copy number and LOH in tumour samples only (no paired samples).When I...
Hi Cheng Is it possible for me to make a copy number summary plot in dChip2005? I had trouble switching to 2006 version with my 100K data and was never able...
Hi!! I am trying to open some CEL files without an associated text file as you recommend in the web page, however, I can not find the "Read SNP call file and...
What kind of information can we get from the list of filtered gene besides that the expression of the genes is over the threshold? What does the another ...
Hi Cheng!! I downloaded the new version and now I am able to specify the box to save SNPS to DCP file, however, when the program try to access the DCP file it ...
hi I noticed dchip suggested to do the gene/row-wise standardization (substract mean) when calculating the smaple cor. matrix, thus eliminate the effects from...
Hi Ellen, You have to use a dchip version number later than what's required for the summary plot function (indicated in the manual). Let me know errors you got...
Hi Alfredo, You need to make sure the genotype call file is saved in text format. Or you can send me the file and error messages for me to check. Cheng ... ...
Hi all, I'm a recent subscriber to dChip yahoo's group. I'm also a mac user. I've done a search within the older message of this group, and i found the one iw...
I use affy mouse 430 array. they have 430a and 430b.cdf file. which one i should use? I tried both, got the same error. I also used conversion tool to convert...
