Ching, You may try the Get external data function: http://biosun1.harvard.edu/complab/dchip/get%20external%20data.htm Let me know how it goes. Cheng ... ...
hi all i found a conflicted data in affy's GCOS output files, and the dchip also give the similar value, it is showed below in GCOS probe 31bsignal 31bPvalue...
Dear Dr. Li: I used your latest dChip for 50 K SNP analysis and get summary plot for inferred copy number. However, I cannot go back to the original chromosome...
Dear Dr. Li: Sorry, it's me again. I output the data into Excel format. I found that usually the data could show both physical position (Mb) and Genetic (cM)...
Dear all, I need to analyze some data coming from Affy 50k Hind and Affy 50k Xba SNP arrays. I know that dChip can handle this kind of data. However, I have...
Dear Dr Ching and dChip users, I am trying to do copy number analysis with an external data. I understand I have to upload a sample file as the provided one. I...
Dear Dr. Li: Is it possible to put the "annotation" into the genome information file so that when we output the data in excel format, it will have a column of...
Xavier, Maybe you are using early access 100K data. You may find their cdf files here: http://biosun1.harvard.edu/complab/dchip/snp.htm Cheng ... From:...
Rehab, You external SNP data file can contain only SNP genotypes, or signal columns before genotype columns (could be empty or “No Call”). Genome info...
Dear Sir: I am using 50K Xba for genotyping. Initially I put 10 pair of normal- tumor samples and several tumor-only samples. For the pair samples, I used the...
I've been using dChip for some time and have been trying for figure out why sometimes I am able to export the Standard Error column and other times I am unable...
I ran the same 6 arrays again in and not-in memory. I verified that the "array" files were different. "in" had values for outlier measurement ,"not-in" had...
Dear Sir: In the new version of dChip, we can display copy number in together with LOH view. However, we can output copy number only in this view. Is it...
Hi Philip, Thanks for the detailed description. Not having SE stored or exported was a consideration to save memory when “Load probe data in memory” is...
Hi Cheng, Sorry, but the problem persists. I did exactly what you said using my 6 test arrays. The subsequent results were different: although the arrays...
Hi evrybody, Is it possible to filter a number of consecutive SNP? I would like to show just the region with N consecutive significant SNP (blue colored labels...
Julien, You may try this: http://biosun1.harvard.edu/complab/dchip/snp.htm#export_data “Chromosome/Export SNP data/Regions with significant curve value”....
Philip, I got the same results using the two options. Did you try the latest version on both options? This version computes all positive expression than the ...
Hi Philip, I found that it's due to that "Open group/Read unnormalized probe data" option is checked in your analysis. In such case, "Analysis/Normalize" will ...
Hi Cheng, Thank you for fixing this problem. I used the new version and all my test cases worked comparing computations in/not in memory when CEL & TXT files...
Dear Cheng, I have had an 'out of memory' error thrown up by DChip while running Chromosome analysis on 97 x Nsp arrays. Is there a limit on the amount of...
Dear Cheng, I am filtering genes with present calls in >20% of the samples and variant across the samples. I am using logged data because I have got outlayers....
Dear Cheng, Is there a quick and straightforward way to measure the level of heterozygosity in X chromosomes of male patients in DChip? (To use as a measure of...
while I'm setting up to run Merlin and Allegro, I tried to run the parametric linkage analysis in dChip. I have 250K SNP results for several families. I did...
Hello,I tried to use DchipSNP on 50k Xba 240 chip, but the software doesn't work without the cdf file, how can I get it?Thanks.Christophe PouletLaboratoire de...
General array/clustering question- can I generate a heat map to compare the expression between the same cell type but different subjects, without comparing to...
hi cheng, in "displaying range of standardized values" i wanted to confirm that the range "-3 to +3" refers to negative values= increasing negative log ratios ...
