Feng, ... sets? Is it "first come, first served"? Yes. ... consistent results concerning the expression index and Present call. This is true. So you may keep...
You may try some suggestions by using "Get external data": To read in cDNA array data, one may put background-adjusted green and red channel signals for one...
Cheng: Is there a way I can ask dchip to use R 1.6 instead of 1.7 since I installed both of them and don't want to uninstall 1.7. Thanks a lot, Jeff ... ...
Fan, Affy has decided to keep the old CEL file format. So I suppose one can export text format CEL files from GCOS and use them with dchip. This tool from Affy...
Mervin, This is a good point. You may try this: delete the corresponding lines of these unwanted probe pairs in CDF file (open it in a text editor): ...
Hi, everybody I am wondering what a universal algorithm/formula to calculate fold change is and if fold change function is available in dChip. Thanks in...
They will most likely be identified as single outliers and treated as missing data: http://biosun1.harvard.edu/complab/dchip/pm%20only.htm#outlier But I think...
Leighton, The major reason is MAS5 and dChip normalizes and computes expression values differently. I think t-test alone is not enough to filter biologically...
Hi, Cheng: I am another new user. Today, I downloaded dchip version 1.3 and also installed the DCF file. The problem is: 1. Why there are no descriptions for...
Hi Yao, thanks for making this question, I am new user too and I have exactly the same problem!! Laura ... From: yaoguo63 [mailto:yaoguo63@...] Sent:...
MBEI is concerned with expression values but not detection calls. I use the calls mostly for P call % at "Filter genes" and "Compare samples", and for these...
Hi, I already downloaded this file, but when I run the program, this file couldn't be open and it said 'probably this file is not saved in tab-delimited text...
Hi, I already solved this problem by unzipping the file. Thanks, Yao ... <http://rd.yahoo.com/M=251812.3856299.5103760.1261774/D=egroupweb/S=1 7057131 ... ...
Hi, Cheng: I downloaded the R and R-COM and run it according to your suggestions, but why no outpuit? Thanks, Yao ... click "Get ... click "Run". ... in R ... ...
Hi, I have a question about PM/MM model to calculate MBEI. Is it more similar to MAS4 or MAS5 algorithm? When I do two sample comparison using both PM and...
Hello, I have a questions on how to combine the gene expression values from U133 A and B chips. Since A and B chips are hybed separately, I am thinking of...
You may refer to this link: http://biosun1.harvard.edu/complab/dchip/combine%20chip.htm#sub_chip ... the average intensity of the 100 control genes on both A...
Thanks, Cheng! I agree that the scaling is not needed for comparing gene expression over multiple chips. But I am trying to study the abundance of genes of...
The absolute expression values are comparable for a probe set across samples (since they are based on the same probes), but not across the probe sets. We can...
I have a question that may be not related to dchip. However, I hope someone could point me to the right direction. Has anybody have done some work (published...
PM/MM model is more sensitive at low end, but can give negative expression values. This same factor can produce unreliable large fold changes (due to small...
... The following papers have compared results from oligo and cDNA chips, often with a third data source such as RT-PCR: * Yuen T, et al. Accuracy and...
Hello, I'm having some trouble figuring out exactly what is happening when samples are compared through Dchip. For illustrative purposes, consider an...
I have 5 samples, of which one is control and 4 are treatment at different time point. My question is how to analyze this data set with dChip such as cluster...
Dchip doesn’t use test but only the threshold of correlation coefficient as cutoff. Cheng ... From: zurich_ma [mailto:christoph.huber@...] Sent: Monday,...
