Hey! I'm very pleased of dChip in microarray data analysis. I have a question though. We have an experiment where some of the chips were run on HG-U133A chip...
Dear All, I am continuously finding missing expression values in the excel table after exporting expression values from dChip. The truncate options when...
Hi, I am a new user of dChip. I am trying to use the 20 probes intensity for each probe set serving as replicates for estimating the errors for gene intensity...
Please make sure files fromm both data types are under the folder that's specified in "Open Group ->Data directory". Also, make sure Date file type is checked...
Thanks Yu, the problem was, that I had "treat array outliers as missing values" checked in options/Analysis................ unchecking this solved the...
Thank you for the reply. It seems to me that Li & Wong used resampling based on the SE reported for each probset to assign confidence to clustering result....
Hi I'm fairly new to GeneSpring and and finding my way around the software however I can't figure out how I can do a paired t-test on my data, if anyone can...
I was wondering if anyone knows whether or not dChip can be used on cDNA expression array data? If so, how can the data be formatted to suit the needs of...
I tried it the way you suggested, but since you have to choose a cdf and gene info file specific for only one chip, dChip can not open these two chips ...
To read in cDNA array data, one may put background-adjusted green and red channel signals for one array as two columns in the data file, and do normalization...
Christine, ... know how dChip works, but not how they work)? Both SAM and dChip uses permutation of group labels to create the "null" comparisons where all...
Hi, I have read the Li and Wong PNAS 2001 paper which describes the model upon which dChip is based. I have a few questions regarding the process of fitting...
Hi Cheng, I've heard recently that dCHIP can call areas of LOH without the need for a normal/tumor pairing. I've used dCHIP to try and call areas of LOH...
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...
Eugenio, After “Analysis/Open group”, make sure you also do “Analysis/Normalize” and “Analysis/Model-based expression” to obtain expression values....
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...
