I believe the original question here is in regard to the p-values associated with the detection calls. MAS output lists the call (P/A) and also the p-value for...
Jim, The p-values from MAS cannot be read or used by dChip. Cheng ... From: jim_rathman [mailto:rathman.1@...] Sent: Friday, July 02, 2004 11:34 AM To:...
Hemali, The MAS4 algorithm (which dchip uses) does not produce p-values, and it uses decision tree to make P/A calls. But MAS5 algorithm computes p-values. ...
I need to mask redundant probe sets in order to do GO analysis. I think the best thing for me to do is to keep the probe set with the lowest SE (as a...
Kirstin, ... sets with the same locus link) is kept? dChip keeps only the first of the probe sets with the same LL ID in a list. Also make sure to check...
I believe there's a bug in the Compare Samples platform. For example, suppose I am comparing one B sample with one E sample and specify only a single criteria:...
George, Affy uses different algorithms for P/A calls (p-values) and expression values. Smaller p-values correspond to Presence calls and more consistent ...
Jim, This is a bug that gives confidence interval [3,3] instead of [-3, -3] for fold change -3, when logged expression values have standard error of 0. Please...
Hello, This email message is a notification to let you know that a file has been uploaded to the Files area of the dchip group. File : /test arrays.xls ...
dchip@yahoogroups.com
Jul 15, 2004 2:44 pm
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Hi, I have converted CEL files from 4 to 3, loaded the genome.CDF file for the mouse genome MOE430_2, and after few seconds of analysis, the excel file shows...
I am attempting to combine the data collected on HG-U133_Plus_2 and HG-U95Av2 Affymetrix Genechips. During the process for exporting the expression values for...
Mountainhighm, It seems your common probe set file contains extra space before probe set name. You can delete the space before “117_at” in the file and...
Hi Cheng, I imported RMA processed data into dChip, so the data are quantile-normalized and in log 2 scale. When I do comparing samples, what do you think...
You should also log2 transform the threshold. E.g. E-B > 1 means two fold. Don’t use E/B or B/E. If the expression values have been log-transformed, E-B and...
Thankyou for the response to my last post. The fix that you suggested allowed me to progress to the gene clustering phase. My first question has to do with...
Mountainhighm, Did you uncheck “Tools/options/clustering/pre-calculate distance” when clustering many genes? If the number of genes is large (e.g. 10,000),...
Thank for the quick response to my previous post. Concerning the PM only question, what I want to know is whether this option will exclude MM probes (which is...
Mingqian, ... redundant ones before the analysis. Does that mean expression of only 1 out of N probe sets of that gene will be considered Yes. ... sets of the...
Dear Cheng, Thanks for the reply. But how do you specify the pairs. If the dChip program do not know which sample pair with which sample, it will be the same...
Dear Cheng, If I have four pairs samples, #1 pairs with #5, #2 with #6, 3 with 7, and 4 with 8. In the dChip, if I list the base line as [1, 2, 3, 4] and...
It will assume the samples specified in E and B groups paired as ordered. Cheng ... From: Tabellini, Laura [mailto:ltabelli@...] Sent: Tuesday, July 20,...
Rebecca, ... genome info hg15.xls" but got the error message "No genome information found for the current chip type; probably wrong genome information file"...
C.Rubioescudero, DChip is developed in VC++, and has codes to call R: http://biosun1.harvard.edu/complab/dchip/interface_r.htm let me know if you will need the...
