I have two questions for comparison between two types of arrays. 1. Can dChip convert GenBank ID or Clone ID into affymetrix probe ID? If so, how to do it? ...
Dear Dr Li: Is it possible to read 100K cel files without the accompany SNP call files? I want to produce an invariantset normalized cel files by dchip, do...
Hi, I read in Mapping10K_Xba142 cel files and the Affy SNP calls. I then open an array list file that has pairs of normals and tumors, with each pair followed...
How does dChip calculate the PC1 and PC2 values generated for its graph and output files? For example, does it use the correlation or covariance matrix? Does...
Is there a version of dChip for mac?? __________________________________________ Yahoo! DSL – Something to write home about. Just $16.99/mo. or less. ...
hi Cheng, I just wanted to clear something up. When Dchip calculates the inferred copy number for a set of samples - does it use only the samples specified in...
Dear Cheng, I am running dCHIP to infer copy numbers on some SNP array samples using a normal reference set. I tried to analyze my samples using both the PM/MM...
Could you tell me how to make a reference file that contains multiple samples? Please also tell me how to use this reference file in the copy number analysis....
There is no dchip version for Mac. cheng ... From: dchip@yahoogroups.com [mailto:dchip@yahoogroups.com] On Behalf Of Mondo Sent: Tuesday, January 10, 2006 8:57...
Hi Wennuan, You should include some normal samples in the group and then specify them by the "Ploidy(numeric)" column in the sample info file. Cheng ... From:...
You may try the "Analysis/Get external data" function. cheng ... From: dchip@yahoogroups.com [mailto:dchip@yahoogroups.com] On Behalf Of saichanma_s Sent:...
Hi Natalie, If "options/trimmed percent" is 0, all samples in the group (may not in array list file) with "Ploidy(numeric)" of 2 will be used as reference ...
dChip cannot directly do these. But you may use NetAffx database for the purpose. Cheng ... From: dchip@yahoogroups.com [mailto:dchip@yahoogroups.com] On...
Hi Dr Li, I am using DChip 2005 to examine 6 Human 133plus2 arrays corresponding to 3 conditions. 3 of the arrays were run some time ago; they are fairly low...
Hi Tarun, From the normalization plot, the invariance set method is working well, so you don't need to do linear scaling before normalization. Cheng ... From:...
Hello! I am new user of DCHIP and this is the first time I am dealing with microarrays and their data. Thus I have some pretty basic questions, and I would...
Hello! I am a new user of dCHIP and microarray data, so I have some pretty basic questions and if someone could help me with these questions, it would be...
Hi Dave, Please unzip this link: http://biosun1.harvard.edu/~cli/pca.zip for related C++ codes in dchip. bool LDA::GetLda() bool LDA::GetPrinComp() bool...
Roberta, You may first cluster these probe sets by "Analysis/Clustering", and then control+click a branch to color it, and finally use "Analysis/Genome" to ...
Federica, Stretch is a set of genes (e.g. all up-regulated) close to each other on the chromosome, so close that this happens more than by random chance and...
Hi Maria, This may be related to the sampling method used for computing the group mean considering measurement variance. When the two groups are combined, the ...
hi are there any Dchip users out there who are doing LOH and copy number analysisusing the 500K chips? I am wondering how other people are doing their LOH...
Dear Cheng Apart from reextracting cdf and cel files, are there any differences in normalization, MBE and final copy number estimation between the f3 and f4...
Hi Charles, There is no other difference between the two versions except the file format so the analysis results will be the same. However the future updates...
Dear List: I have been trying to make a Gene information file for a custom equine array which Affymetrix made for our laboratory. I am trying to perform ...
Tzachos, You can make a gene info file like this file format: http://biosun1.harvard.edu/complab/dchip/hg_u95a%20gene%20info.xls and save in text file to use...
Dear Dr. Li: Thank you for your quick response. I will give it a try. Regards, Tiffy Zachos ... Behalf Of ... equine ... perform ... followed ... file in ... ...
