-----Original Message----- From: bioconductor-request@stat.math.ethz.ch [mailto:bioconductor-request@stat.math.ethz.ch] Sent: Friday, March 21, 2003 6:06 AM To: bioconductor@stat.math.ethz.ch Subject: Bioconductor Digest, Vol 1, Issue 271 Send Bioconductor mailing list submissions to bioconductor@stat.math.ethz.ch To subscribe or unsubscribe via the World Wide Web, visit https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor or, via email, send a message with subject or body 'help' to bioconductor-request@stat.math.ethz.ch You can reach the person managing the list at bioconductor-owner@stat.math.ethz.ch When replying, please edit your Subject line so it is more specific than "Re: Contents of Bioconductor digest..." Today's Topics: 1. Re: Bioconductor Digest, Vol 1, Issue 270 (Nicholas Lewin-Koh) 2. Affy package ?s (sorry for the repost) (Luckey, John) 3. Re: Affy package ?s (sorry for the repost) (Ben Bolstad) 4. mva functions (Jason Skelton) 5. Re: mva functions (Laurent Gautier) ---------------------------------------------------------------------- Message: 1 Date: Thu, 20 Mar 2003 05:04:06 -0800 From: "Nicholas Lewin-Koh" <nikko@hailmail.net> Subject: [BioC] Re: Bioconductor Digest, Vol 1, Issue 270 To: bioconductor@stat.math.ethz.ch, bioconductor@stat.math.ethz.ch Message-ID: <20030320130406.7C6822697B@www.fastmail.fm> Content-Type: text/plain; charset="iso-8859-1" Hi, I don't think this is a g77 error, this is a linker error. I use redhat linux myself so I don't know much about the mandrake distribution. I would suggest first following Laurent's advice and make sure that the readline libs are installed on your system. As Laurent also comments nothing in bioconductor is dependent on hexbin. But this will soon change and hexagons will rule the world, na just kidding. If installing readline and readline_devel doesn't help email again and i will see if we can't get this debugged. Nicholas > Message: 1 > Date: Wed, 19 Mar 2003 17:10:23 +0100 > From: "buhard Ceph" <buhard@cephb.fr> > Subject: [BioC] Install problem of some BioConductor packages > under > linux R session > To: <bioconductor@stat.math.ethz.ch> > Message-ID: <001f01c2ee32$0d520610$4d05030a@cephb.fr> > Content-Type: text/plain > > Hi all, > > > > I encounter some problems while trying to install BioConductor packages > under R for Linux (perhaps as a new Bioconductor user, and not a linux > expert !). > > I've downloaded the tar.gz file sources of Bioconductor and successfully > installed a part of the bundle... but installation stops at 'hexbin', > with an error indicating '-lreadline' is nof found, as reported here : > > > > After R CMD INSTALL treated 'graph' package, I get the following messages > : > > * Installing *source* package 'hexbin' ... > ** libs > g77 -mieee-fp -O3 -fomit-frame-pointer -pipe -mcpu=pentiumpro > -march=i586 -fno-fast-math -fno-strength-reduce -O3 -fomit-frame- pointer > -pipe -mcpu=pentiumpro -march=i586 -fno-fast-math -fno-strength- reduce -c > hbin.f -o hbin.o > g77 -mieee-fp -O3 -fomit-frame-pointer -pipe -mcpu=pentiumpro > -march=i586 -fno-fast-math -fno-strength-reduce -O3 -fomit-frame- pointer > -pipe -mcpu=pentiumpro -march=i586 -fno-fast-math -fno-strength- reduce -c > hcell.f -o hcell.o > g77 -mieee-fp -O3 -fomit-frame-pointer -pipe -mcpu=pentiumpro > -march=i586 -fno-fast-math -fno-strength-reduce -O3 -fomit-frame- pointer > -pipe -mcpu=pentiumpro -march=i586 -fno-fast-math -fno-strength- reduce -c > herode.f -o herode.o > g77 -mieee-fp -O3 -fomit-frame-pointer -pipe -mcpu=pentiumpro > -march=i586 -fno-fast-math -fno-strength-reduce -O3 -fomit-frame- pointer > -pipe -mcpu=pentiumpro -march=i586 -fno-fast-math -fno-strength- reduce -c > hsm.f -o hsm.o > g77 -mieee-fp -O3 -fomit-frame-pointer -pipe -mcpu=pentiumpro > -march=i586 -fno-fast-math -fno-strength-reduce -O3 -fomit-frame- pointer > -pipe -mcpu=pentiumpro -march=i586 -fno-fast-math -fno-strength- reduce -c > htst.f -o htst.o > gcc -shared -L/usr/local/lib -o hexbin.so hbin.o hcell.o herode.o hsm.o > htst.o -L/usr/local/lib -L/usr/lib/gcc-lib/i586-mandrake-linux- gnu/3.2 > -L/usr/lib/gcc-lib/i586-mandrake-linux-gnu/3.2/../../.. -lreadline -ldl > -lncurses -lfrtbegin -lg2c -lm -lgcc_s -L/usr/lib/R/bin -lR > /usr/bin/ld: cannot find -lreadline > collect2: ld returned 1 exit status > make: *** [hexbin.so] Erreur 1 > ERROR: compilation failed for package 'hexbin' > [root@localhost root]# > > > > None of all subsequent packages is installed then. > > Maybe there's something missing on my OS (mdk 9, kernel 2.4.19-24) ? Or a > library with a bad (or missing) path declaration ? what else ? > > Any help greatly appreciated > > thanks in advance. > > > > BUHARD Olivier > INSERM U434/CEPH > 27 rue Juliette DODU > 75010 PARIS > > > [[alternate HTML version deleted]] > > > ------------------------------ > ------------------------------ Message: 2 Date: Thu, 20 Mar 2003 11:42:05 -0500 From: "Luckey, John" <john.luckey@joslin.harvard.edu> Subject: [BioC] Affy package ?s (sorry for the repost) To: <bioconductor@stat.math.ethz.ch> Message-ID: <ab77297d38b3b24c903dbfb2bbbbd7c8021338@mail2.joslin.harvard.edu> Content-Type: text/plain; charset="utf-8" Hello Bioconductor Users, Sorry to bother you, but I have a couple of quick questions on the affy package that I have been unable to answer by reading through the textual description of affy available on the bioconductor website and the recent papers on the subject. Iin general, am very impressed with the noise reduction using affy and truly appreciate the Bioconductor open source concept and packages available. I am trying to compare directly our own homebrewed data normalization within Splus (splining of affyIDs (post MAS summing of probes)) with the rma output. Question 1: Are the values output by rma to eset (and written to tab delimited file with write.exprs) the logbase2 of the "actual" affyID values, or are they the affyID values themselves. This is obviously important for comparing rma to our old methods, and for estimates of "accurate" fold change estimates- It seems to me that rma is much more precise in that much of the noise between replicates, especially at the low end, seeems to have been reduced in rma, but I am struggling with how to estimate back to accurate fold change estimates. Question 2: Is there an easy way to write out the PM values to tab delimited file post background correction and normalization (to assess individual probe sets prior to median polish). I am trying to work out reasons for differences between our old method and rma for individual affy IDs. Sincerely, John Luckey C John Luckey, MD PhD Post Doctoral Fellow - Benoist-Mathis Lab Joslin Diabetes Center One Joslin Place, Rm. 474 Boston, MA 02215 phone: (617) 264-2783 fax: (617) 264-2744 e-mail: john.luckey@joslin.harvard.edu ------------------------------ Message: 3 Date: 20 Mar 2003 09:19:00 -0800 From: Ben Bolstad <bolstad@stat.berkeley.edu> Subject: Re: [BioC] Affy package ?s (sorry for the repost) To: "Luckey, John" <john.luckey@joslin.harvard.edu> Cc: bioconductor@stat.math.ethz.ch Message-ID: <1048180740.1645.120.camel@bmbbox.dyndns.org> Content-Type: text/plain > > Question 1: Are the values output by rma to eset (and written to tab delimited file with write.exprs) the logbase2 of the "actual" affyID values, or are they the affyID values themselves. This is obviously important for comparing rma to our old methods, and for estimates of "accurate" fold change estimates- It seems to me that rma is much more precise in that much of the noise between replicates, especially at the low end, seeems to have been reduced in rma, but I am struggling with how to estimate back to accurate fold change estimates. > The values given by the rma() function are log base 2. Working in log base 2 you could take differences and then take 2^(difference) to get fold changes. Or you could just take 2^(rma expression value) and take ratios if you prefer. You might find that RMA estimated fold changes are attenuated compared to other methods. That is that the estimated fold change is smaller than that computed using other methods. But the noise reduction at the low end is pretty dramatic. > Question 2: Is there an easy way to write out the PM values to tab delimited file post background correction and normalization (to assess individual probe sets prior to median polish). I am trying to work out reasons for differences between our old method and rma for individual affy IDs. If you manually background correct and normalize (as individual steps), doing something like data <- ReadAffy() data.bg <- bg.correct.rma(data) data.norm.bg <- normalize(data,method="quantiles") in each case pmdata.bg) and pmdata.norm.bg) will give pm matrices after preprocessing. Investigate the function write.table() for outputting the data to tab delimited files. thanks, Ben ------------------------------ Message: 4 Date: Thu, 20 Mar 2003 18:16:38 +0000 (GMT) From: Jason Skelton <jps@sanger.ac.uk> Subject: [BioC] mva functions To: bioconductor@stat.math.ethz.ch Message-ID: <pine.osf.4.44.0303201809270.138580-100000@pfes1.internal.sanger.ac.uk> Content-Type: TEXT/PLAIN; charset=US-ASCII I'm trying to use the mva functions dist & hclust however after a while I get the following message: TypVSNdist <- dist(typVSN, method = "euclidean", diag = FALSE, upper = FALSE) Error: cannot allocate vector of size 589776 Kb > typVSNcluster <- hclust(dist(typVSN@h)) Error: cannot allocate vector of size 589776 Kb I'm running R in linux, any help much appreciated regards Jason ------------------------------ Message: 5 Date: Fri, 21 Mar 2003 03:29:33 +0100 From: Laurent Gautier <laurent@cbs.dtu.dk> Subject: Re: [BioC] mva functions To: Jason Skelton <jps@sanger.ac.uk> Cc: bioconductor@stat.math.ethz.ch Message-ID: <20030321022933.GB7797941@genome.cbs.dtu.dk> Content-Type: text/plain; charset=us-ascii Dear Jason, We would need to know a bit more about your settings, like what one get by doing 'dim(typVSN)' or 'object.size(typVSN)', and also the amount of RAM your machine has.... Hopin' it helps, Laurent On Thu, Mar 20, 2003 at 06:16:38PM +0000, Jason Skelton wrote: > > > I'm trying to use the mva functions dist & hclust > however after a while I get the following message: > > TypVSNdist <- dist(typVSN, method = "euclidean", diag = FALSE, upper = > FALSE) > Error: cannot allocate vector of size 589776 Kb > > > typVSNcluster <- hclust(dist(typVSN@h)) > Error: cannot allocate vector of size 589776 Kb > > I'm running R in linux, any help much appreciated > > regards > > Jason > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor -- -------------------------------------------------------------- currently at the National Yang-Ming University in Taipei, Taiwan -------------------------------------------------------------- Laurent Gautier CBS, Building 208, DTU PhD. Student DK-2800 Lyngby,Denmark tel: +45 45 25 24 89 http://www.cbs.dtu.dk/laurent ------------------------------ _______________________________________________ Bioconductor mailing list Bioconductor@stat.math.ethz.ch https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor End of Bioconductor Digest, Vol 1, Issue 271