User: Rafael A. Irizarry

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Posts by Rafael A. Irizarry

<prev • 63 results • page 1 of 7 • next >
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Answer: A: Trouble in making the cdf package for Arabidopsis?
... if you are using windows you need to get the tools to make window packages or contribute the package to bioconductor. they will do it for you. rafael On Mon, 3 Mar 2003, Hua Liu wrote: > Thanks for the help. I got the cdf file of the Arabidopsis ATH1 array (ATH1-121501.cdf) and tried to make t ...
written 14.7 years ago by Rafael A. Irizarry630
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Comment: C: Try to run a lots of chips: 32 bits vs 64 bits
... one way to get around it is to write a function that does RMA but reads only the PMs. If you learn R it wont be that hard. reading only the PMs will reduce the memory use by more than 1/2. RMA doesnt use MMs. if you decide to do this, email me and ill help as long as you contribute the final product ...
written 14.7 years ago by Rafael A. Irizarry630
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Answer: A: normalization question
... if i were analyzing this, my first attempt would be to use quantile normalization on all arrays at once. by default, you cant normalize 133A and 133B together so you would have to separate these. On Sat, 1 Mar 2003 Phguardiol@aol.com wrote: > Hi all, > I am pretty new in this list so I hope ...
written 14.7 years ago by Rafael A. Irizarry630
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Answer: A: Bioconductor cdf package for Arabidopsis?
... if you have the cdf file, you can use the package makecdfenv to make you own. if you do bioconductor would appreciate you contribute it. On Sat, 1 Mar 2003, Hua Liu wrote: > I want to study the probel level data from Affymetrix Arabidopsis Genome ATH1 Array. I loaded the agcdf pachage, but the ...
written 14.7 years ago by Rafael A. Irizarry630
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Re: makecdfenv
... are you using msft windows? the makecdfevn package makes source code which in unix/linux can be installed using R INSTALL. to do this in windows you need to get some special utilities (see the R windows FAQ). if you submit the source code to bioconductor they can create a windows package. On Mon, ...
makecdfenv written 14.7 years ago by Rafael A. Irizarry630
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Answer: A: how to get a cdf envirment file
... thats not the described file. its http://www.bioconductor.org/data/cdfenvs/cdfenvs.html On Tue, 25 Feb 2003, Huang, Cheng-Cheng (NIH/NCI) wrote: > Hi, > > I need a cdf environment file for HG_U95A, > The directed site http://www.bioconductor.org/data/cdfenvs.html does not > work. ...
written 14.7 years ago by Rafael A. Irizarry630
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Answer: A: problems attaching affy library
... what happens if you try the same thing in a directory with no .RData? some objects from version 1.0 are not compatible with version 1.1. On Thu, 20 Feb 2003, Mahlet Tadesse wrote: > > I have installed the Bionconductor package in my directory and am > attaching the libraries in my R sessi ...
written 14.8 years ago by Rafael A. Irizarry630
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Answer: A: ANOVA performance
... not (yet) integrated to bioconductor, but it might be what you are looking for: http://www.jax.org/staff/churchill/labsite/software/anova/rmaanova/ind ex.html On Wed, 19 Feb 2003, Isaac Neuhaus wrote: > Is there a recommended package to run ANOVA. The generic functions in R perform > very p ...
written 14.8 years ago by Rafael A. Irizarry630
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Answer: A: Question on normalization
... i dont know about a concensus but... if you look at how different replicate arrays can be (see Figure 2 here http://www.biostat.jhsph.edu/~ririzarr/papers/affy1.pdf), it seems impossible to argue that over-all differences in intensities are due to biological variation as opposed to obsucuring variat ...
written 14.8 years ago by Rafael A. Irizarry630
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Answer: A: Image() - Question
... if ab is an AffyBatch object you can type image(ab,transfo=NULL) ## or image(ab,tranfo=function(x) x) to see all arrays in the batch in linear scale. alternatlvely, you can type image(ab[[i])) to see array i. ab[[i]] is a Cel object (a lower level class). image(ab[[i]]) calls the imaging function ...
written 14.8 years ago by Rafael A. Irizarry630

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