User: Yair Benita

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Yair Benita80
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12 years, 11 months ago
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Posts by Yair Benita

<prev • 8 results • page 1 of 1 • next >
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customCDF name not recognized and switched to Affy CDF
... Hi All, For a while I have been using these lines below to normalize a large Affy data set with customCDFs and gcrma. I can't seem to make it work anymore. For some reason, in the affinity adjustment of gcrma, there is a switch to the affy CDF which gives an error later. Its a bit puzzling. I am co ...
cdf affy gcrma written 8.6 years ago by Yair Benita80 • updated 8.6 years ago by James W. MacDonald51k
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Limma -time course - no replicates
... Hi Naomi, Thank you for pointing out this example, its really useful. Can you explain the meaning of the p.value and F.p.value in this case? Which one should be used? time=1:10 design=model.matrix(~time) fit=eBayes(lmFit(data, design)) Thank you. Yair on 6/8/10 3:53 PM, Naomi Altman at naomi at ...
regression limma written 9.3 years ago by Yair Benita80
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Comment: C: Fixing brainarray repository link for mac os x
... Hi James, Thanks a lot - this works great. The reason I had issues with it is that installing manually at system level did not work. When running gcrma, it kept trying to download the files. When I installed manually at user level it started working. Setting the options("pkgType") to source works gr ...
written 9.9 years ago by Yair Benita80
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Fixing brainarray repository link for mac os x
... Hi All, I am a fan of the brainarray customCDF and now routinely normalize my Affy files with these CDFs. I find the annotation much more reliable than Affy's. I typically use GCRMA after reading the CEL files. On the mac I install these customCDFs manually from source. GCRMA has the ability to fetc ...
annotation go customcdf cdf gcrma written 9.9 years ago by Yair Benita80 • updated 9.9 years ago by James W. MacDonald51k
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Custom CDF Version 12 is released
... Dear Manhong, I would just like to note here my own experience installing v12 on R 2.9.1 on MacosX. Using the R package installer I selected "Other Repository" and used the URL: http://brainarray.mbni.med.umich.edu/bioc/ Next I installed several custom CDF files in binary format and got the followin ...
cdf written 10.3 years ago by Yair Benita80 • updated 10.3 years ago by Manhong Dai200
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Normalizing two different platforms
... Dear R members, I have this problem with 2 different Affy platforms. We started the experiment with U133A chips but had to switch in the middle to U133A_plus2. All the U133A are backordered with no delivery in sight. The two chips have the exact same gene probes and differ only in a few control prob ...
cdf affy gcrma written 11.7 years ago by Yair Benita80 • updated 11.7 years ago by Kasper Daniel Hansen6.4k
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Help with limma experiment design - two color data
... Hi All, I have two color microarray data (genepix format) from patients with cancer. I have a variable number of replicates per patient and in some cases a dye-swap. On each slide we compared the RNA from tumor tissue to RNA from healthy tissue in the same patient. Going through the limma documenta ...
microarray limma written 12.5 years ago by Yair Benita80
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How to read and normalize hundreds of CEL files?
... Dear Bioconductors, I am trying to read and normalize 230 microarray CEL files (Affy U133A). This is obviously very difficult since it requires a lot of RAM and always fails with an alloc error. I tested it on a dual Xeon (2.3Ghz) linux machine with 4Gb of RAM, but failed at the ReadAffy command. E ...
microarray gcrma written 12.9 years ago by Yair Benita80 • updated 12.9 years ago by James Anderson820

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