User: A.J. Rossini

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A.J. Rossini810
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Posts by A.J. Rossini

<prev • 81 results • page 1 of 9 • next >
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Answer: A: Loess normalization for Agilent chips
... Why not just use Limma and the corresponding tools? It's FAR easier that way. That way you actually get what you pay for, rather than far less... "Malard, Joel M" writes: > I am struggling to get data from Agilent cDNA arrays into BioConductor. > It seems to me much easier to get the ...
written 14.2 years ago by A.J. Rossini810
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Answer: A: error in getBioC("exprs")
... Robert Baertsch writes: > Better yet, it would be nice if these incantations were on the > bioconductor website. We are waiting for someone to write them! Alternatively, I thought that a BioC-installer package for Debian exists (at least on the recent Quantian bootable DVDs, I think). be ...
written 14.2 years ago by A.J. Rossini810
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Answer: A: error in getBioC("exprs")
... You can compile R without being root. Why not just do that? i.e. unpack, then ./configure --prefix=/home/your/placement/directory for example... best, -tony Robert Baertsch writes: > While you are at it, can you please allow people to install R without > being root? Our sysadmin ...
written 14.2 years ago by A.J. Rossini810
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Answer: A: Macroarray Image Analysis (summary)
... "Nicholas Lewin-Koh" writes: > I did notice in the archives that Anthony Rossini was looking into > making an R-package for Jimage. For various reasons, I'm not going to be doing that. best, -tony -- Anthony Rossini Research Associate Professor rossini@u.washington.ed ...
written 14.3 years ago by A.J. Rossini810
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Answer: A: Filtering genes using a list
... mcolosim@brandeis.edu writes: > Quoting "A.J. Rossini" : > >> mcolosim@brandeis.edu writes: >> >> > Jim, >> > >> > Thanks for the hint about %in%, where did you find this function? I >> couldn't >> > find any thing about it. >> >& ...
written 14.3 years ago by A.J. Rossini810
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Answer: A: Filtering genes using a list
... mcolosim@brandeis.edu writes: > Jim, > > Thanks for the hint about %in%, where did you find this function? I couldn't > find any thing about it. ?%in% should provide the help page. It does for me (though under Emacs). (i.e. help("%in%") ) Interesting that help.search("in") isn't to ...
written 14.3 years ago by A.J. Rossini810
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Answer: A: Harsh results using limma!
... "michael watson (IAH-C)" writes: > I am extending the argument to the larger case where I might have plenty > of replicated experiments and still want to find significant genes > amongst sub-populations. I've had one e-mail which shows that this is > possible, so I am happy. > > ...
written 14.3 years ago by A.J. Rossini810
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Answer: A: Harsh results using limma!
... Argh. You can't really draw conclusions (even discovery) with biological variation from three animals without bringing in extra information. Suppose you don't have extra information. Think about the possibilities of the next 3 animals. under a conservative assumption that half the population is ...
written 14.3 years ago by A.J. Rossini810
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Answer: A: Harsh results using limma!
... The OTHER explanation could be technician error or inadvertent cross-hybridization due to processing; the catch is that you've also got a batch effect, it seems. The more critical issue is that you've got to use statistics that describe what you want. Obviously, those that standardize location (m ...
written 14.3 years ago by A.J. Rossini810
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Answer: A: GOStat and multiple testing
... Might want to look at the social network literature -- something like a p-* model for adjustment of the variance, and possibly looking at the adjoint graph (flipping nodes/edges) might produce reasonably adjusted coefficients. best, -tony Nicholas Lewin-Koh writes: > Hi, > I have been th ...
written 14.3 years ago by A.J. Rossini810

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