David, If you use "Tools/Export expression" to export SNP signal data, then use "Get external data" to read back (uncheck "SNP array"), you can use "Compare ...
Hi Cheng, Just a quick question/problem regarding exporting of SNP data. I am interested in exporting regions with a specific threshold (significance curve...
Hi Cheng, Related to my previous question about exporting significant regions, I noticed this function doesn't work at all for raw CN. Is this correct?? This...
Hi Peter, I have seen similar situation. Hom in normal and Het in tumor often indicate genotyping errors, and it occurs simultaneously with intervening changes...
Dear Dr Li, I normalized a dataset of about 400 U133 plus2 chips and now need to normalize additional 210 chips. I may need to integrate this 210 chip dataset...
Aiguo, Dchip can handle 2000 arrays as hard limit. It’s depending on memory practically. You can uncheck “Open group/options/load probe data in memory” ...
Dr. Lr, That is helpful and thank you so much, Aiguo Ehen, I have 3G memory on my machine. It was ok for me to normalize 360 chips, but when it comes to 550...
Dear Dr. Li, In an additional sets I need to normalize U133 A and B of 200 chips. I like to use PM/MM model. The .cdf files are separated for chip A and chip...
Hi Aiguo, You can use the method here to combine two arrays instead of pasting: http://biosun1.harvard.edu/complab/dchip/combine%20chip.htm#sub_chip You can...
Hi Judith, The pedigree file should include all founders. Here individual 0 is not in pedigree. If person 2-4 have a common parent not genotyped, he/she is a ...
Hi, In DChip yuo have the choice to normalize to the chip that has the median intensity. Is it possible to normalize to a median reference chip. That is to say...
Hi Martin, Such function is not available. However if you create an artificial median array by other means, you can include it in dchip for analysis. Cheng ......
Hi, Chen, I have 11 chips with unnormalized Median Intensities: 98, 95, 122, 93, 92, 94, 97, 93, 121, 91, 105. When I did the normalization using D-Chip, I...
wenbo xu
wenboxu@...
Nov 8, 2006 4:53 pm
2361
Wenbo, What do you mean by “cutoff”? Usually all arrays could enter further analysis after normalization. Cheng ... From: dchip@yahoogroups.com...
Hi, Cheng, sorry for this. Cut off here means : In the "model based expression..." step, there is a chooice for "Truncate low values to()". I used 100 as that...
wenbo xu
wenboxu@...
Nov 8, 2006 9:30 pm
2363
hi cheng, was wondering if you could implement a "Find sample" search the same way you have the "Find gene" probeset search function. If it could be added to...
Hello All, I am a first year PhD student at the John Innes Centre and have just started analyzing my microarray data generated from the Affy Wheat Chip. I am...
Sorry for the simple question: Are the GO structure files that are linked to in the dChip manual specific for a certain array type (mouse/human) or are they...
hi,i also want to do this kind normalization, do you know how to make a artificial median reference chip. is this kind normallization similar to the AFFY...
hi ,haletufn, you could download the celfileconversion file from AFFY's website, and convert your cel file, so dchip can read the bioformat cel file. or if you...
hello Cuiling Lee, thank you for your answer. I have read the manual very carefully but as it is my first time analysing such data with no help it is all...
Hello Hale, I think the Affy cel file conversion tool is for changing between the ascii and binary file types Affy has used with various versions of MAS5/GCOS....
Hi Hale, They are applicable to all arrays. I have always used the 'deprecated' GO files. Sincerely, David Carter ... -- David Carter London Regional Genomics...
There is a method for generating the TXT files from GCOS. It was explained to me, so I never looked for it in the documentation. After doing File:Analyze for...
Hello David, Thank you so much for your reply, it has really helped. I do have the .CHP files from the core lab, they are in .CHP format though. Can I convert...
Dear Phillip, Thanks! I will try to convert to .txt as you described. I do have the RPT files from the lab that hybridized the chips so I may try to use those...
I open the .CHP files in GCOS press the save icon on the toolbar to save a .txt file, but I agree, doing it one by one is annoying. ... -- David Carter London...
