Hello, anybody I am just wondering how to filter out all the common genes/overlapped genes, which are found among treatments, and separate out them from other...
Anyou, You can sort genes in Excel by LocusLink ID. Or check "Tools/Options/Analysis/Mask redundant probe set", and then cluster this list of genes. Then...
Hi, all, I download dChip and some data file yesterday. But I need a whole picture about this software. What are the main functions? What files are needed and...
Hi, I was wondering if a background correction was performed (by dchip) before normalization and modeling. I am trying to perform a dchip style analysis in...
Ann, In dChip the background correction happens after normalization and before PM-only (but not PM/MM difference model) model-based expression. See here for...
Hi, I have been using the chromosome view for SNP data successfully for some time and now I would like to look at expression data in this visualization. ...
Colin, The latest dChip: http://biosun1.harvard.edu/~cli/dchip2004.exe handles the expression array in a similar way of SNP array copy number analysis. You can...
Cheng, Thanks for your quick reply. I have tried the new version with a ploidy column and I get multiple columns. I still have the same problem though......
Hi Cheng, I have some 100K SNP data and would like to use dChip to identify LOH and copy number. I wonder whether dChip can handle 100K SNP data. Thanks. KK...
Hi, I am a dChip user and have a question about normalization. I sent this question to Cheng Li early today but think I may get more help by posting it here. ...
Hi All, Can somebody explain why i get this error message and how to get rid of it. Thanks in advance. Hrishikesh {Open group PrbData Reading CDF file...
Hi All, I figured out what was the error, but the following error beats me, i file which i specified exists in the said location!!!! Hrishikesh {Open group...
Hello: Why would a file be called "L3.real.CEL.txt". It should just be a .CEL file, I would think. the .CDF file has to match the species of the .CEL file, but...
It's true that CDF file can be anywhere. If you downloaded the CEL files from a website and used "save target as" option, the default is to save as txt file....
Dear Cheng, Thanks for the prompt reply, indeed that was the problem. I moved from Xp to 2000 and i changed the path everywhere except in the working...
If you want to use the MAS generate Present calls (instead of the calls generated by dChip), then place the MAS txt files in your working directory. If there...
Ruty, Since there are only two samples, genes are standardized to be always -0.7, 0.7 (approximately) or 0.7, -0.7 in the two samples before clustering and ...
Hello, I just downloaded the latest DChip version and I performed some comparison analyses. My problem is that the DChip value of the t-test does not equal my...
Hi, all, Could anyone who really know dChip do us a favor and organize the posts, so that all important questions and reponding answers gathered together? I...
Paul, See this page: http://biosun1.harvard.edu/complab/dchip/compare%20sample.htm#group_mean "Pooling arrays is mainly for down-weighting the unreliable...
Hi, Cheng It seems to me that the differences between Affy and dChip vis-a-vis background correction are the following: (1) Affy divides the array into 4 x 4...
Lizhe Xu
lxu@...
Oct 11, 2004 5:12 pm
905
Hello After I normalized and modeled my arrays, I exported the expression values. I was suprised to find some negative signal values (15 to 60 genes per chip)....
Hello, I am having a problem getting DChip (version 1.3 10/6/04) to interface with R. Before I installed DChip, I installed R 1.9.1 and DCOM 1.35. I know they...
