Hi. Cheng, I have 18 Affy chips for 3 treatments, 6 chips in each treatment. The correlation within treatment group is high, R values are about 0.96- 0.98 and...
Hi all, I'm trying to read in raw HU133A chip data (I have both the .cel and .dat files) with dChip 1.3 (I downloaded it on 3/2/04). I tried opening the group...
Fingermytuna, You may use text editor to open a converted CEL file to check its header line to make sure the array type (e.g. HU133A.1sq), or paste the header ...
Hi Cheng, Thanks for your quick reply. I checked the headers from the .cel files and they all (4 of them) were HU133A.1sq I also checked the corresponding DAT...
Cheng, Would you mind sending me a link to download the older v1.2? I've used it in the past and never had any trouble. It would be good to verify that the...
You should use HG-U133A.cdf file instead of HG-U133A_tag.CDF. See CDF files here: http://www.affymetrix.com/support/technical/libraryfilesmain.affx cheng ... ...
Hi I have set the tgt value in Affy to be 100 for all my arrays. Is there need to normalise arrays in dCHIP? I want to read the MAS5 present and absent...
Hi, I am trying to create a gene informationf file for HGU133A and B. I downloaded the CSV files from NetaFFx, unzipped them and also downloaded the Gene...
Clare, If you have scaled expression values in MAS5 and check “Open group/Use MAS5 Signal” to use MAS5 expression values in TXT files, you don’t need to ...
HI I seem to have a problem with dCHIP 1.3. The program opens fine and I can open a group... but it won't run when I select "compare samples". All other...
Hi, I'm new to the analysis and after a day's effort of downloading all data and application files, I'm stuck again ... after entering all files for analysis...
Is there “Modelled” sign in the lower-right corner? If not you need to do “Model-based expression” first to obtain expression values. Cheng ... From:...
Hi Cheng Yes the data is modelled (I read in MAS5 signal). Even if I calculate MBEIs in dCHIP the compare samples function doesn't work. Clare ... to do ... ...
I am wondering how to select which factors to use for ANOVA. The field to choose a file is greyed out. Has anyone used this feature yet? What format does...
David, Yes factors should be specified in “sample info file”. See this link for examples: http://biosun1.harvard.edu/complab/dchip/timecourse.htm Cheng ......
David, Yes factors should be specified in “sample info file”. See this link for examples: http://biosun1.harvard.edu/complab/dchip/timecourse.htm Cheng ......
I am doing analysis of a project in which I have 2 treatments (one experimental, one control), each with three time points. Each time point is made of three...
Charles, You may export data by “Tools/Export expression data” and then do this in Excel. E.g. first compute the average of three 0h samples, and then...
Hey! I enjoy very much using the dChip, but I have a question. How does dChip calculate the p-values for GO-terms in a cluster? What is the equation? Thanks in...
Dear Dr. Li, I want to apply dChip to normalize my chip data. There are 7 groups (conditions) of dataset, 4 chips in each group. If i want to get the...
Hi, I am a new user of dChip and have a query which we have been debatting in our lab. I have loaded the files into dCHIP and was originally normalising to the...
Hi, I am a new user of dChip and would like some thoughts on which is the best model to use. I have carried out comparisons using the PM model and the PM/MM ...
Xinzhong, You can use the default baseline array (check image to make sure it doesnt have severe image contamination). ... it necessay to normalise all the...
hi cheng, i wonder how i can export the picture of the cluster tree puls annotation and affy-code to a powerpoint or photoshop file. whenever i try it i only...
Chris, ... tree puls annotation and affy-code to a powerpoint or photoshop file. You can use "View/Export image" or select an branch and use "Clustering/Export...
Joni, It’s based on hyper-geometric distributions. Please see this link for details: http://biosun1.harvard.edu/complab/dchip/clustering.htm#gene_cluster ...
