Hello Cheng, I have a question about exporting information of those probes sets identified as 'array outliers'. So if an array has >5% probe sets as 'array ...
Thanks Cheng! Apparently the current/latest version of Dchip does not export the outliers as empty entries. I tried to use an older version (10/2005) and it...
Hi Cheng, we have just run some Human exon arrays and are having trouble running dChip with them. We find that dChip crashes when it tries to load the .pgf...
Cheng There appears to be a limit to the number of characters/length of line of the SNP annotation detail shown at the bottom of the dChip window when viewing...
Dear Dr Cheng, I am doing copy number analysis using dChip. I have uploaded the combined normalized intensity for each individiual through get external data....
Rehab, This is a testing function. To compute total copy numbers, you can use these default values: Do not check “Analysis/Normalize&Model/Options/Compute...
Does anyone have or know if a good tool to display extent of deletions and amplifications against an ideogram? For example, one chromosome on the middle, with...
Hi Cheng, I think there is a bug in the latest version when attempting to export regions above significant curve value (HMM copy number), the regions exported...
Dear Cheng, I found an interesting linearity correlating to gene expression kinetic when I perform PCA on samples taken from different time point. I would like...
Hello everyone, I am currently using dChip 2006_12, and it seems that it is not compatiable with the R version currently I am using: 2.3.1 So, I have to...
Nozomi, The gene list you specified in dchip are used. I recommend you use lda() function in R directly to obtain loading information. Cheng ... From:...
Statistical Microarray Analysis Using R at Imperial College London, during March & April 2007. **PLEASE NOTE THAT WE ALSO PROVIDE STATISTICAL ADVICE ON A...
Dear Cheng, dear dChip users, A question regarding the allele sharing analysis: As a result of this analysis some of the proteins are highlighted in blue. I...
I am a new user of dchip2005_f4. I am trying to analyze affymetrix 250K nsp chip and I don't succed in generating the CSV file necessary for this chip....
Hi Sébastien, If you download genome information file from here: http://biosun1.harvard.edu/complab/dchip/snp.htm specify it at “Analysis/Chromsome”, not...
Dear Cheng and everyone, I am in chromosome view and I oomed in alot. It is taking a very long time to scroll through. It won't zoom back. Any suggestions? 2...
Richard Friedman
friedman@...
Mar 15, 2007 5:17 pm
2641
This is a 100K analysis. When performing Analysis/Chromosome, I am not seeing the chromosome icon or the gene list. I only see the Samples and SNP names. The...
I finally found it: (from the manual) In the "Proportional distance" display, the genes are displayed with their relative screen distances proportional to real...
Hello! Could somebody tell me where I can download this 2 files for my 10K 2.0 Array SNP Genome Information File: - 11_k_snp_genome_info_hg15_AFAMfreq.xls -...
Hi, Is there a possibility to save the haplotyp view. Because when I close dchip and start new, the haplotyp view is absent (grey). (LOD curve is displayed!) ...
Dear Cheng, I have duplicated the results of Zhao et al nov, H1395t . I got 9 as in the paper. However I did not see a plot peak, indicating amplification of...
Richard Friedman
friedman@...
Mar 20, 2007 10:11 pm
2649
Hello, I have tried to run a linkage analysis on all chromosomes for two 250k nsp chip, but my run lasted like forever. I wonder if this is normal or if my...
Sébastien, dChip linkage analysis hasn’t been tested on 250K SNP arrays. I recommend that you look into other software for analysis, or try dchip allele...
