Hello, I am using the U133_Plus_2 chips and am having trouble parsing the CSV file. Below are the errors I am getting. Any suggestions? Many thanks, Marcy ...
Dear Cheng, When normalizing U133 results of patients and controls together, typically I got a bifurcate scatter plot between a patient and a control (please...
Dear Cheng: I am about to analyze my Affy DAT files using dCHIP, however, after reading dCHIP manual, I kind get the impression that MAS is probably better in...
Dear Cheng, Thanks. I downloaded the latest .exe file, but I am still getting the following error when I attempt to "make information file" (the gene ...
Marcy, Please try this updated one with larger limit: http://biosun1.harvard.edu/~cli/dchip.exe Thanks very much for pointing out the issue. Cheng ... From:...
Hi I want to generate one gene list file of present calls only for 27 arrays. Is this possible and if so how do I do it? I wan to be able to use this file...
I would like to compare the results from several different normalization and expression estimate value calculation methods. I used dChip for normalization and...
I am looking for a simple way to take multiple probe lists and parse the data to construct and display venn diagram-like figures with lists of common/unique...
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Hello, On one of my GeneChips I have an obvious local contamination. Now I read dChip's manual section "Image contamination correction" about the two possible...
Hi Cheng, When I tried to drag the slide bar at the far right of the clustering window, the heat map will bounce back to the top at about 3/4 of the sliding...
I think it depends on where you selected gene is located. If the gene you highlighted is on top, the heatmap will always go back to the top. ...Tao sbbmu...
I tried it again. But it was not the case. I selected one gene near bottom and also select a branch including it, it still bounced to the top. I could not even...
Bing, You can press the “ESC” key to deselect a data point (blue or red color), or click a data point at the bottom and then use arrow keys to zoom and...
... I emailed you the chip image with the contamination and you replied that this was total image contamination so gradient correction would not help and that...
Hello, In the documentation of the RMA ("Robust Multi-Array Average") algorithm I read the following note: "Note that this expression measure [= the RMA...
I would say it depends how you are going to filter your genes. If you are going to use t-test, you probably want to go with log transformed data because log...
No, you can import expression levels in any scale into dChip (and use its analysis features), you just won't be able to use its normalization or use it to...
When the contamination is semi-transparent (e.g. http://biosun1.harvard.edu/complab/dchip/image%20correction.htm) gradient correction could be useful. ...
... I use to filter by p values (based on t-tests) as well as fold changes. And yes, you are right in that for pure fold change filtering it would be easier to...
... Normalization and calculation of expression estimates have already been performed by the RMA algorithm, so these steps would not be necessary anymore in...
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