Hi, I have found the same problem in the results of sample comparison - missing probe set description/infos (setting Options doesn't help). The previous...
Thank Cheng for your help on P/A calls. I'm still doing some comparions between dChip and MASv5. I found that more genes are called out to be significant in...
Seongjoon, ... good! How many samples do you have for each group? When the group size is small, it’s also good to use “Analysis/Compare samples/Combine...
Dear Group, Maybe this question has been asked before, but I couldn't find it and don't recal it being discussed at the d-chip web page. What is the level of...
Can someone briefly explain the data output from the FDR calculation in dChip 1.3? Also, a broader question... is there any solid thresholds for acceptable...
Colin, DChip FDR computation is based on permutation. So that we know after permuting the group labels, how many genes are “falsely” discovered in such ...
Jorg, I think having 4 arrays is moderately ok (2 is not good). DChip still tries to cross-compare the 4 arrays to identify outliers and compute expression ...
My experiment has 4 replicates. After looking at the data and sample cluster, I think one replicates labeled wrong, that is one should be in control group...
Hello, all, A question related to this thread: which should be used for clustering? log transformed values or untransformed values? Wenbin Wei Division of...
Wenbin, You may try both to see which gives results better agreeing with known facts. E.g. whether replicates or samples in similar conditions cluster ...
Hi, I am a new user of dChip. I have a rather basic question. I've been struggling with the gene information files. Following the manual, I downloaded the...
Anybody got a spare HG-U133B.CDF file hanging around that I can ftp down to my PC? I need one to get dCHIP to work on some 133B data. I have the HG-U133A.CDF...
Did you download the geneinfo files for dchip 1.3+, but using dchip 1.2? Probably that's the problem. ...Tao asmann_yan <asmann_yan@...> wrote: Hi, I am...
Mike, This is because "Tools/Options/Analysis/Consider measurement error when average" is checked. As a result the differnce values between pairs are reversed...
Hi, Has anyone upgraded from R 1.6 to R 1.7.1 and is still able to run LDA and PCA plots in dChip? I cannot get dChip to generate graphics through R 1.7.1...
He is looking for the actual cdf file, not a Bioconductor affy environment. dChip will not be able to use the files you are linking to here. Jim James W....
Morgen, You may need to restart the computer after installing R 1.7.1 for it to add registry key of R path. Afterwards if needed redo R-COM setup. Let me know...
Li, Is there a way to get the right fold change estimates (point and interval) when log levels are selected? If not it would seem to be something simple to...
Stephen, Currently at "Compare samples" you may use the mean difference threshold (criterion 2) as fold change when the data is log transformed (If the ...
Greer, This probably indicates that some background-subtracted PM values are 0. You may use PM/MM view to look at the probe data of the probe set. Also you can...
Hi, I just started learning using d-chip. Do I need to change my data file type to CEL or DAT file from XLS file before I input my data? Thank you, Mandy...
Mandy, The answer is no. If you already have XLS files containing expression values, you can use the “Get external data” function (first save your data ...
Hi, I have successfully gotten external data from XLS file. Would I be able to view the array image, PM/MM data, and model-based expression indexes with this...
