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User: Malard, Joel M

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Posts by Malard, Joel M

<prev • 10 results • page 1 of 1 • next >
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How to use affy's image function on RMA values?
... Greetings, I would like to compare (visually) the raw intensities of 40 affymetrix MOE430A arrays with the corresponding expression values computed by RMA, e.g. using the function image. It seemed a good idea to replace the exprs component of the AffyBatch object with the exprs component of the o ...
written 13.7 years ago by Malard, Joel M100 • updated 13.7 years ago by Ben Bolstad1.1k
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Answer: A: CRANrepository is not a repository or some http problem
... Sorry for the delay. It seems like the problem is sorted out. On my system at least, two metadata packages (zebrafish and xenopuslaevis) are needed by annotate but not loaded by getBioC(); so annotate fails to install and then the affy package fails too. Another possible problem is that I was using ...
written 14.0 years ago by Malard, Joel M100
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CRANrepository is not a repository or some http problem
... I am not able to install (the development version of) BioConductor. I moved my office across the campus to this problem may be a local. Thanks for any pointer, Joel Malard > install.packages2("rankProduct") Warning message: cannot open: HTTP status was `404 Not Found' Note: http://www.biocondu ...
written 14.0 years ago by Malard, Joel M100
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Batch effects and linear models
... This is a naďve question. Is there some BioConductor package to estimate mixed models on Affymetrix data? I have a 2 x 2 design, treatment versus control at two labs. There are strong (lab) batch effect that can be seen by clustering the data. So far I have computed RMA (and GCRMA) values for each ...
clustering written 14.0 years ago by Malard, Joel M100 • updated 14.0 years ago by Fangxin Hong810
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Run r codes in shell?
... On Unix and Linux the following commands will work as well: R --no-save < file.R R --save < file.R What is most helpful though is: R --help Cheers, Joel -----Original Message----- From: bioconductor-bounces@stat.math.ethz.ch [mailto:bioconductor- bounces@stat.math.ethz.ch] On Behalf Of G ...
nem written 14.0 years ago by Malard, Joel M100
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Writing MAList to file (limma)
... Hi, Is there a natural way to write normalized MA values along with the correct probe names? One can write the M and A values as tables but the row indices need not match the order of the probe names in the CEL files. Thank you for your help and my apologies if this is a trite question, Joel M. M ...
probe written 14.4 years ago by Malard, Joel M100 • updated 14.4 years ago by michael watson IAH-C3.4k
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Answer: A: Weight functions for Agilent chips (limma)
... Hi Giovanni, Sorry, being new to R programs, it took me some time to parse your own. Could something of the sort be useful to you? wtAgilent.mRGOLFilter <- function(qta) { mapply(min,1-qta[,"gIsFeatNonUnifOL"],1-qta[,"gIsFeatNonUnifOL"], 1-qta[,"gIsBGNonUnifOL"],1-qta[,"g ...
written 14.4 years ago by Malard, Joel M100
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Weight functions for Agilent chips (limma)
... Dear All, I was wondering what other people have been using for the weight function in read.maimages with Agilent arrays? I tried the following: wtAgilent.GFilter <- function(qta) { qta[,"gIsPosAndSignif"] } wtAgilent.RGFilter <- function(qta) { (qta[,"rIsPosAndSignif"]+qta[,"gIsPosAndSignif ...
normalization written 14.4 years ago by Malard, Joel M100
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Answer: A: Loess normalization for Agilent chips
... Thank you for pointing this out. I had not seen that read.maimages() can process 'agilent' files and thought all the data structures had to be filled in manually. Best wishes, Joel -----Original Message----- From: A.J. Rossini [mailto:rossini@blindglobe.net] Sent: Friday, September 17, 2004 12:5 ...
written 14.4 years ago by Malard, Joel M100
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Loess normalization for Agilent chips
... I am struggling to get data from Agilent cDNA arrays into BioConductor. It seems to me much easier to get the data in affy's normalize.loess() than in the other cDNA array packages. Given that "one who get a bargain get what he pays for", does anyone has comments, recommendations or warnings to sh ...
written 14.4 years ago by Malard, Joel M100

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