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 ...
Aeonlanack, They represent standardized values of non-logged raw expression values for each gene. See below for details. Cheng “Before clustering, the...
Hi Marc, In dchip, you can do normalization and modeling as usual (if needed use only the samples you want to cluster at an “Open group” session, since...
Dear dChip users, I am learning to use dchip for copy number, I am working onthe data of Zhao et al , Cancer research 64, 3060/ I can get the LOH and copy...
Richard Friedman
friedman@...
Feb 6, 2007 11:44 pm
2558
Cheng and other dchip users, Upon the initial "Open Group" I got an error message to the effect, Cannot find array named 'HCC1187t' and 5 other array names are...
Richard Friedman
friedman@...
Feb 7, 2007 5:39 pm
2559
Hi Rich, You are right about the reason. The first column of sample info file has to match exactly with the CEL file names. I probably modified some CEL file ...
Hi, When I run analysis-->genome, the analysis is completed but then it crashes when the diagram appears. How can I prevent this? Thanks, Marc ... Don't be...
Hi Marc and Charlotte, Thanks for letting me know the issue. This is a bug introduced in version 3/16/06+. Please use this 2/9 version to correct it: ...
Greetings, When filtering array data using analysis-->filter, in general how does one decide what limits to set for variation range, %P call, and expression...
Marc, I usually use 20% P call and 0.5 to 1.5 sd/mean to get about 500-1000 genes for clustering. Expression value magnitudes are gene dependent, so I usually ...
Hi everyone, If I could follow up on Marc's questions, if my primary interest is to get a list of genes that are changing significantly in one condition...
Hi, I'm using dChip to heatmap a bulk of values I obtained from uptake assay (not microarray) data, which range from single digit to 1000s values. I notice I...
Dear dchip users. I am trying to reproduce the results of Zhao et al ifor copy number. During the normalize step, my job froze at HCC38t. I have the cel file ...
Richard Friedman
friedman@...
Feb 13, 2007 10:43 pm
2573
Hi Rich, You may try either uncheck "Analysis/Normalize/View norm plot", or remove that cel/dcp file out of directory, or try this latest dchip: ...
Hi Cheng, I seem to be having an issue when attempting to infer LOH using HMM (considering haplotype). In previous versions of dChip, this function would...
Dear Cheng and dChip user community, I am using the latest version dchip on the Zhao 2004 dataset and I am having trouble reading in the cel files. I get an...
Richard Friedman
friedman@...
Feb 20, 2007 10:21 pm
2577
Hi Rich, You can check array summary file exported by dchip at "Open group". Check if the file contains the "HCC1395 june" sample. Or are only DCP files but...
Hi, I have tested the new dchip release (http://biosun1.harvard.edu/~cli/dchip2006.exe) and a problem appears when I do a linkage analysis. All steps are ok...
Julien, This was a bug. Please try this 2/14 version: Http://biosun1.harvard.edu/~cli/dchip2006.exe In this version you want to toggle “Chromosome/Draw...
Ag55, Please do not use non-academic language in this group. I removed Julie’s advertising message promptly as soon as it’s posted. I have unsubscribed...
