Hi Cheng, Is there a function in dCHIP to identify significant regions of LOH with a corresponding neutral copy number? We are working with a fairly large...
Hi Jacques, Here is a gene info file with minimal columns: http://biosun1.harvard.edu/complab/dchip/hg_u95a%20gene%20info.xls You can copy and paste your...
Hi Paul, You may try this updated dChip: http://www.dchip.org/manual.htm After “Analysis/Chromosome”, use ‘D’ to go to the copy number view, select ...
Hi Paula, Depending on the bit of the pedigree. If it’s <= 18 dChip can analyze it (dChip reports this when you use “Chromosome/Linkage analysis”). What...
Hi Cheng, I Have a question about normalizing data across chips. One of my Hind arrays has relatively low median intensity of 675. The array that Dchip chooses...
Hi Natalie, You may use the latest version: Please use the updated dChip here: http://www.dchip.org/manual.htm on the right side of the normalization plots (4...
Dear Cheng and members of the dChip community after using dChip for more than half a year without issues I started to get the following problem that keeps...
Hi Ovidiu, ANOVA or t-test select genes gene-wise so don't consider their biological relationship (e.g. GO) with other genes. So this p-value is trying to...
Hi Charles, This is due to a recent change that added a "dbSNP" column in the 2nd column. Please update to the corrected dChip: http://www.dchip.org/manual.htm...
Hi Peter, Normalization will make the arrays to have similar overall brightness. The median probe intensities will be close but not exactly the same. From your...
Hi Cheng, I am trying to analyze Staphylococcus aureus GeneChips, but when trying to open the group, I get the following message: Converting CDF file...
Hi Jorg, I compiled a special dChip version that can handle up to 1000 probe pairs: http://biosun1.harvard.edu/~cli/dchip2005_p1000.exe Please let me know if...
Hi Yun, Thanks for letting me know the issue. What array type and gene information files are your colleague using? I only develop and test dChip on Windows...
This is about the function below. I corrected a bug that made previous dChip always use 0% trimmed mean of all samples when "Trimmed pct" is not 0. ... ...
Dear All, I am looking for a recessively inhereted single gene in an extended family with apparently unique phenotype. There are 5 affecteds in 3 sibships. ...
Hi, I get this error message (see below) when I am trying to compare my samples accross chip types (U133A and U95Av2). I have followed the instructions in the...
Jessica Lindvall
jessica.lindvall@...
Nov 7, 2005 4:08 pm
1352
Hi Kemal, There are 6 parents and 4 grandparents (whose relationship is not known?) with 5 affected, so the number of bit (2*#non-founder - #founder) is around...
Hi Samin, Since there are two samples in the control and two samples in the comparison groups, the number of possible permutations is very small (6 different ...
Hi Cheng, I am getting an error message "Number of chategories of column "Cohort Id" exceeds limit" (Cohort Id is a field in my sample information file) ...
Hi Jai, The limit is 50 categories for each sample information column (how many categories do you have?). If this column is not essential to display, you can...
Hi Roberta, I haven't tried this. But You may row-wise combine the genome info file of gene array and SNP array (save in text file) and try. Let me know how it...
Hi Cheng, Thanks for the information. The number of chategories are more than 50. And I need it for comparing different cohort (groups) However I can...
I have been trying to get the optional refGene and Cytoband files for Drosophila Melanogaster from the website mentioned on the dChip website. I do not see ...
hi cheng, please could you point out in which reference you explain how Dchip algorithm works that calls the SNPs from the PM/MM intensity values? thanks ...
Hi Natalie, dChip does not make SNP calls. Instead, at “Open group” it looks for paired txt files (with CEL files) that contain Affymetrix SNP calls. ...
Hi Roberta, They should be the same. The difference probably is due to the default display of copy number. In dchip2005 it’s the median-smoothed copy number ...
Dear Dr. Li, Thank you for making dChip such a user-fiendly software. Our programmer is trying to help me convert binary CEL files from the GCOS server to text...
