User: Vawter, Marquis

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Posts by Vawter, Marquis

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AffyRNAdeg slopes
... Hi Jim, just a follow-up to your post, when you referred to outliers on the density plot in discussing AffyRNAdeg slopes, is this a function within the AffyRNAdeg program? Best wishes, Mark "Anyway, in my experience, large differences in slope are less critical than big differences between the dens ...
written 13.0 years ago by Vawter, Marquis70 • updated 13.0 years ago by James W. MacDonald45k
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RNA degradation (Chris Paulse)
... Hi Chris, we have seen the same phenomenon with affyRNA degradation plots. There is definitely a smooth trend, until the last point. It is very reproducible, in fact this position should show the highest intensity overall, but shows about 50% of what would be expected. Best, Mark -----Original Me ...
microarray normalization cancer probe roc limma process written 14.3 years ago by Vawter, Marquis70 • updated 14.3 years ago by James W. MacDonald45k
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Older version of R and affy package
... Hi, I am working with some R scripts that seem to call the older version of affy (maybe 1.0) and R 1.5.1. When upgrading the affy package to 1.1, I seem to have lost the ability to run older R scripts that use the affy 1.0 version. Is there an archive of R and affy that would allow users to keep usi ...
affy written 15.0 years ago by Vawter, Marquis70
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Answer: A: hist and mva.pairs problems
... I have d/l the latest R1.6.1 and Affy 1.1 Attached is a histogram from newly U95A chips. It seems that the basic histogram function is gone, and the mva.pairs function keeps giving the error: Error in log(x, base) : Non-numeric argument to mathematical function There seems to be major problems wit ...
written 15.0 years ago by Vawter, Marquis70
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hist and mva.pairs problems
... This message is in MIME format. Since your mail reader does not understand this format, some or all of this message may not be legible. ------_=_NextPart_000_01C29CD0.B6529030 Content-Type: text/plain; charset="iso-8859-1" I have d/l the latest R1.6.1 and Affy 1.1 Attached is a histogram ...
affy written 15.0 years ago by Vawter, Marquis70 • updated 15.0 years ago by Rafael A. Irizarry630
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BioConductor 1.1 installation problem
... I am working in R.1.6.1 under win98 and was trying the getBioC() installation. I get the following error messages and am not able to complete the installation. Afew days ago there was no problem with the installation on my office computer, so I am puzzled. Thanks for the efforts to make these packa ...
biobase repostools affy written 15.0 years ago by Vawter, Marquis70
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biobase
... Hi--I d/l the biobase package today and could not get the affy.pdf file to open up. C:\Program Files\R\rw1050\library\affy\doc\affy.pdf Also, there seems to be some problem with using the new Bioconductor package to work with biobase and affy. Best, Mark Marquis P. Vawter, Ph.D. Department of Psy ...
biobase affy written 15.6 years ago by Vawter, Marquis70 • updated 15.6 years ago by Laurent Gautier150

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