Hi, I am presently using dChip to analyze Affy 10K SNP (early access) chip data. I am attempting to do some clustering on my samples. I have been able to...
Thanks Cheng. Is there an efficient way,using dChip, to take the probe sets that are generated in the cluster analysis and trace them back to their location...
Analysing the same array-results with dChip and CCNT give different results. A deletion is easily confirmed but a very good visible duplication in CCNT is...
http://biosun1.harvard.edu/~cli/dchip2004.exe ... -- David Carter London Regional Genomics Centre Robarts Research Institute, Room 4.01 PO Box 5015, 100 Perth...
Hi, Cheng Thanks. Sorry, I might not make it clear in the last post. Actually, I would like to export the base signal for a whole probe set as one value in one...
I have about 30 "metrics" files from a collegue I am trying out against my arrays. all arrays discussed are on U133A chip. I do not have the CEF files for...
Hi, I am having trouble with DChip (version 1.3 on Windows XP Professional). I would like to map a short list of genes to their corresponding chromosomal...
Hi, I am trying to use a msk file with CEL files from the hgu133atagcdf, but keep getting a message whether I use a MSK file or a txt file: "No matching MAS...
Hi again, Looks like the MSK file or txt file is read, but the whole probesets that are in the MSK files are entirely delected. I just wanted to mask...
I am trying to compare expression data from new U133_plus chips with old U133A chips. In order to do this, I would like to generate a "common probe set file",...
Hello to everybody, I was using the gene information file downloaded from the http://biosun1.harvard.edu/complab/dchip/info_file.htm. I have been working with...
Hello dChippers, I am trying to load SAGE expression files to dChip. The files are 2 columns, tab-delimited text: tag_sequence, tag_count. The number of tags...
Hi, My name is Jennifer and I am curently analysing data from HGU95aV2 gene chips. I have used dChip to sort my genes of interest into gene ontology...
Hi I am using the dCHip gene ontology function to sort genes into their relevant gene ontology categories. I am interested in the genes which have no gene...
Lana, dChip mask file will mask out the whole probe sets. Check "Tools/options/Analysis/Allow txt file to contain unknown probe set" to get around this error...
Sean, You may consider exteranl data file: http://biosun1.harvard.edu/complab/dchip/get%20external%20data.htm But dchip has a limit of analyzing < 100K genes. ...
Hi All, I have a list of probeID's (300) with their x,y coordinates. I have 250 odd .CEL files in dchip, how do i query for PM and MM intensity for the list of...
Dr. Cheng Li, I don't want all the probes with their PM,MM for a given probe set ID, i want given a probe set ID and x,y coordinates what is the PM and MM...
Thomas, My impression is that U133A is a subset of U133_plus and have the same probe set names. If that's the case, you can just use U133A probe set names as...
Dr. Li, We have customized Affy chips that have both human and mouse genes. We know some of the probes will cross hybridize and want to exclude them from the...
