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From Limma to SAM

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utepandragon@tiscali.it ▴ 50

@utepandragontiscaliit-476

Last seen 10.2 years ago

Gordon wrote: >This isn't an error in limma of course, rather you have tried to use a >function (write.table) on an inappropriate object. Do you want to output >the normalized log-ratios? If so, you might try >write.table(MA$M, file="your_file.txt",sep="\t") I've tried write.table(MA$M, file="your_file.txt",sep="\t") and it's OK, but i'd like to output my normalized-between-array (unlogged or Log2) data to SAM. Is it possible? __________________________________________________________________ Tiscali ADSL SENZA CANONE, paghi solo quando navighi! E in pi? il modem e' GRATIS! Abbonati subito. http://point.tiscali.it/adsl/index.shtml

limma limma • 1.2k views

ADD COMMENT • link updated 21.0 years ago by Gordon Smyth 51k • written 21.0 years ago by utepandragon@tiscali.it ▴ 50

score 0 · Answer 1 · 2003-12-02

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Gordon Smyth 51k

@gordon-smyth

Last seen 23 minutes ago

WEHI, Melbourne, Australia

> Gordon wrote: >>This isn't an error in limma of course, rather you have tried to use a > >>function (write.table) on an inappropriate object. Do you want to >> output > >>the normalized log-ratios? If so, you might try >>write.table(MA$M, file="your_file.txt",sep="\t") > > I've tried write.table(MA$M, file="your_file.txt",sep="\t") and it's OK, > but i'd like to output my normalized-between-array (unlogged or Log2) > data to SAM. Is it possible? I suggest you ask the SAM people Gordon _________________________________________________________________ > Tiscali ADSL SENZA CANONE, paghi solo quando navighi! > E in pi? il modem e' GRATIS! Abbonati subito. > http://point.tiscali.it/adsl/index.shtml

ADD COMMENT • link 21.0 years ago Gordon Smyth 51k

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Hi, all-- I wanted to start a thread on R speed/benchmarking. There is a nice R benchmarking overview at http://www.sciviews.org/other/benchmark.htm, along with a free script so you can see how your machine stacks up. Looks like R is substantially faster than S-plus. My problem is this: with 512Mb and an overclocked AMD Athlon XP 1800+, running at 588 SPEC-FP 2000, it still takes FOREVER to analyze multiple .cel files using affy (expresso). Running svm takes a mighty long time with more than 500 genes, 150 samples. Questions: 1) Would adding RAM or processing speed improve performance the most? 2) Is it possible to run R on a cluster without rewriting my high- level code? In other words, 3) What are we going to do when we start collecting terabytes of array data to analyze? There will come a "breaking point" at which desktop systems can't perform these analyses fast enough for large quantities of data. What then? Michael Benjamin, MD Winship Cancer Institute Emory University, Atlanta, GA

ADD REPLY • link 21.0 years ago Michael Benjamin ▴ 120

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I you really want to restart a thread on this, I think "R-help" is the much more appropriate place, since this is really an R topic, not a bioconductor one. Best regards, Martin Maechler <maechler@stat.math.ethz.ch> http://stat.ethz.ch/~maechler/ Seminar fuer Statistik, ETH-Zentrum LEO C16 Leonhardstr. 27 ETH (Federal Inst. Technology) 8092 Zurich SWITZERLAND phone: x-41-1-632-3408 fax: ...-1228 <><

ADD REPLY • link 21.0 years ago Martin Maechler ▴ 330

score 0 · Answer 2 · 2003-12-05

> Gordon wrote: >>This isn't an error in limma of course, rather you have tried to use a > >>function (write.table) on an inappropriate object. Do you want to >> output > >>the normalized log-ratios? If so, you might try >>write.table(MA$M, file="your_file.txt",sep="\t") > > I've tried write.table(MA$M, file="your_file.txt",sep="\t") and it's OK, > but i'd like to output my normalized-between-array (unlogged or Log2) > data to SAM. Is it possible? On reading your question again, I'm guessing that you're wanting the normalized single-channel red and green intensities. Is this right? If so, you can get them from RG <- RG.MA(MA) (see the last section of the Limma User's Guide) where MA is the normalized MAList object, then write RG$R and RG$G to file. Or possibly form cbind(RG$G,RG$R) and write that to one file. I do not know what the SAM software wants as input. Checking that is of course your responsibility. Gordon