In my impression MAS5 is pretty picky about header and footer (e.g. [OUTLIER] section), as well as the standard deviation and number of pixel columns. A safe...
Hello, I want to combine the data for different mouse chipe types: Mu11KsubA(or B) and MG-U74Av2. From mannual, I knew the "common probe set file" need to be...
You may use the following steps to combine the data of the 3 array types: http://biosun1.harvard.edu/complab/dchip/combine%20chip.htm#sub_chip Cheng ... From:...
Hi, Cheng: I can find the common genes of MuG74Av2-other array types by "Make information files", but it didn't work for MuG74Av2-Mu11K, it always said...
Hi, Cheng: It seems no common probe set between MU11K and MGU74Av2, since dChip always said 'Did not find any orthologous/homologous probe set pairs'. But...
Yes in Affy CSV files links are not provided within the same species for different arrays. You can use Microsoft Access to obtain such information by linking...
Hi, I just found out that the Gene Ontology annotation of the old geneinfo file (version1.2) is very different from the NetAffx annotation. I mean "VERY". ...
It's better to use the latest gene info files, which are based on NetAffx. Cheng ... From: Yan Asmann [mailto:asmann_yan@...] Sent: Wednesday, October...
Dear Cheng, I just downloaded HuGeneFL annotation csv file from affymetrix and tried to make a gene information file for that chip in dchip 1.3 (7/10/03)....
Jeff, This is due to that in the Oct 2003 Affy CSV files the ortholog/homolog information has been moved to a separate file. Please use the latest dchip: ...
Dear chen, I'm new to Affymetrix DNA-chip technology and searching for further information or dokumentation about the content of a cdf file (e.g. how can be...
It’s a text file and you can open it to check its format. There are columns of Pbase and Tbase, and when they are the same, it’s MM probe: (PBase != TBase)...
Hi, Dr. Cheng I am wondering how to input the viral GO term (http://www.geneontology.org/gene-associations/gene_association.vida) into dchip and how to use...
... (http://www.geneontology.org/gene-associations/gene_association.vida) into dchip and You may convert GO IDs into words terms and save it in a column of...
hi, I'm new to dChip and am having a problem getting the software to take in my DAT files. I have 9 chips in total and dChip will take in 2, 3 and sometimes 5...
It’s likely that the DAT files are not of the same array type. You may open them in a text editor and get the array type information from the header lines...
Dear Cheng: I got a bounch of data, some of them have replicates, so it is OK to have SE. But severals only have one sample, how did the SE come from? ...
Hello, I am trying to take the information contained in a saved cluster tree and interpret the clustering data for my samples for use in a separate gene...
In the saved tree file, “weight” is the number samples in a branch (or super_sample), and distance is 1 – correlation (default measure of distance) and...
Thanks. Am I right that Dchip multiplies the correlation value by 2 to get that range [0,2]? --Rick ... (or ... distance) ... height of the ... tree ... ...
hi I've tried to open the DAT files in a text editor like you suggested but they won't open. I know that all the 9 DAT files are HG_U95A chips. Do you know...
hi Cheng, I have managed to get dchip to read in all my CEL files, thank you. I have another query..... I have gone through the HG_U95A and HG_U95av2 specific...
hello, thanks for the quick response! I have converted CHP files to TXT which are located in the same files as CEL files. I do not have any apparent problems...
We are looking for anyone interested in purchasing a brand new SpotBot Personal Microarrayer. It appears to be brand new and in perfect condition. It comes...
We are looking for anyone interested in purchasing a brand new SpotBot Personal Microarrayer. It appears to be brand new and in perfect condition. It comes...
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