Just a short question, how does limma and limmaGUI cope with NA values? Or even does it? Thanks for your help, Liz -----Original Message----- From: bioconductor-bounces@stat.math.ethz.ch [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of bioconductor-request at stat.math.ethz.ch Sent: Friday, July 22, 2005 5:00 AM To: bioconductor at stat.math.ethz.ch Subject: Bioconductor Digest, Vol 29, Issue 21 Send Bioconductor mailing list submissions to bioconductor at stat.math.ethz.ch To subscribe or unsubscribe via the World Wide Web, visit https://stat.ethz.ch/mailman/listinfo/bioconductor or, via email, send a message with subject or body 'help' to bioconductor-request at stat.math.ethz.ch You can reach the person managing the list at bioconductor-owner at 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. PLIER: two questions (Ariel Chernomoretz) 2. Re: PLIER: two questions (Adaikalavan Ramasamy) 3. Re: PLIER: two questions (Ariel Chernomoretz) 4. NA and quantile normalization (Ravi Murthy) 5. Re: NA and quantile normalization (Ben Bolstad) 6. AffyPLM for Windows (lucia Garc?a) 7. Spikein Data Package Win32 download problem still present (M.A. Bijl) ---------------------------------------------------------------------- Message: 1 Date: Thu, 21 Jul 2005 11:37:14 -0400 From: Ariel Chernomoretz <ariel.chernomoretz@crchul.ulaval.ca> Subject: [BioC] PLIER: two questions To: BioConductor_list <bioconductor at="" stat.math.ethz.ch=""> Message-ID: <200507211137.14168.ariel.chernomoretz at crchul.ulaval.ca> Content-Type: text/plain; charset="us-ascii" Hi, Just a couple of questions about plier a) With justPlier it is possible to specify as an input vector the replicate structure of the batch we want to analyze ('replicate' input option). Can anybody tell me how this information is used by the algorithm? In fact, can anybody point me to some technical references on how plier works? b) I found that the 64-bit compiled version of plier presents some stability issues (i.e. it crashes). A couple of month ago Adai posted a message (http://files.protsuggest.org/biocond/html/9034.html) saying that he solved a similar (I hope) problem. So, Adai, Crispin, anybody, could you please point me in the right direction in order to make plier run under my 64-bit Opteron? Thank you Ariel./ -- Ariel Chernomoretz, Ph.D. Centre de recherche du CHUL 2705 Blv Laurier, bloc T-367 Sainte-Foy, Qc G1V 4G2 (418)-525-4444 ext 46339 ------------------------------ Message: 2 Date: Thu, 21 Jul 2005 18:29:55 +0100 From: Adaikalavan Ramasamy <ramasamy@cancer.org.uk> Subject: Re: [BioC] PLIER: two questions To: Ariel Chernomoretz <ariel.chernomoretz at="" crchul.ulaval.ca=""> Cc: BioConductor_list <bioconductor at="" stat.math.ethz.ch=""> Message-ID: <1121966995.6531.13.camel at ramasamy.stats> Content-Type: text/plain I had the problem when I was submitting it to a cluster. When I actually ssh-ed into one of the nodes and ran the code interactively, it worked fine. But then I tried with different array type, I had the segment fault even with only 3 arrays. So I am not sure if this is a problem with the cluster queue manager or plier or gcc or something else. Crispin was quite helpful in suggesting to run it interactively, so I hope he finds a solution for you. But I eventually decided not to use PLIER expression measure simply because no documentation was available explaining it. I prefer knowing what I am doing than using a black box systems. I suggest you try RMA or GCRMA which has excellent documentation and has been shown to be better than MAS 5.0 (which is also well documented). Regards, Adai On Thu, 2005-07-21 at 11:37 -0400, Ariel Chernomoretz wrote: <snip> > b) I found that the 64-bit compiled version of plier presents some stability > issues (i.e. it crashes). A couple of month ago Adai posted a message > (http://files.protsuggest.org/biocond/html/9034.html) saying that > he solved a similar (I hope) problem. > So, Adai, Crispin, anybody, could you please point me in the right direction > in order to make plier run under my 64-bit Opteron? ------------------------------ Message: 3 Date: Thu, 21 Jul 2005 14:41:12 -0400 From: Ariel Chernomoretz <ariel.chernomoretz@crchul.ulaval.ca> Subject: Re: [BioC] PLIER: two questions To: ramasamy at cancer.org.uk Cc: BioConductor_list <bioconductor at="" stat.math.ethz.ch=""> Message-ID: <200507211441.12853.ariel.chernomoretz at crchul.ulaval.ca> Content-Type: text/plain; charset="utf-8" I found some technical info about plier in an oral presentation from E. Hubbell. You can find it at: http://mbi.osu.edu/2004/ws1materials/hubbell.ppt However, I agree with you and think will wait for more documentation in order to use plier as a production tool. Thanks for your time Ariel./ On July 21, 2005 01:29 pm, Adaikalavan Ramasamy wrote: > But I eventually decided not to use PLIER expression measure simply > because no documentation was available explaining it. I prefer knowing > what I am doing than using a black box syst -- Ariel Chernomoretz, Ph.D. Centre de recherche du CHUL 2705 Blv Laurier, bloc T-367 Sainte-Foy, Qc G1V 4G2 (418)-525-4444 ext 46339 ------------------------------ Message: 4 Date: Thu, 21 Jul 2005 13:59:59 -0500 From: "Ravi Murthy" <ravidmurthy@hotmail.com> Subject: [BioC] NA and quantile normalization To: bioconductor at stat.math.ethz.ch Message-ID: <bay104-f114ff849a830c350c2ce9da8d60 at="" phx.gbl=""> Content-Type: text/plain; format=flowed Hi, I am new to R, I am doing quantile normalization with a data consisting of a matix 384 X 124. While using "normailze.quantiles" I find that it introduces 'NA' into some of the cells, where we should expect a numerical value, can someone help me to overcome this problem ? The matrix consists of 62 plates in repliccate, and quantile normailization is done for the data from replicates (colomn 1,2) using normailze.quantiles function from 'affy' package resulting in data output as g1 >g1 <- normalize.quantiles(exprs(MSExpr[,1:2])) etc., uptp g62 This command works well for smaller series of data, but while using for a larger data matrix, it introduces "NA" in the place where it is suppose to geneerate data . It doesn't make any sense because elsewhere in the colomn consisting of similar values it computes properly. In addition, if I continue to perform median normailzation of the quantlies, the function fails to give any output, execept for those colomns which does not have any "NA". I cannot get rid of interference of NA in median normalization by using any of NA related functions. I am using R in MAC based platform for this analysis. Please suggest me some way to avoid 'NA' related computation problem. Ravi ravidmurthy at hotmail.com _________________________________________________________________ Dont just search. Find. Check out the new MSN Search! ------------------------------ Message: 5 Date: Thu, 21 Jul 2005 18:12:20 -0700 From: Ben Bolstad <bolstad@stat.berkeley.edu> Subject: Re: [BioC] NA and quantile normalization To: Ravi Murthy <ravidmurthy at="" hotmail.com=""> Cc: bioconductor at stat.math.ethz.ch Message-ID: <1121994740.5357.7.camel at localhost.localdomain> Content-Type: text/plain If your data initially has NAs then it is quite probable that normalize.quantiles() would introduce additional NA (or more likely turn the entire matrix into NA) since it does not make special allowances for NA values. I think the normalizeQuantiles() function in the limma package handles NA's more appropriately. Ben On Thu, 2005-07-21 at 13:59 -0500, Ravi Murthy wrote: > Hi, > > I am new to R, > I am doing quantile normalization with a data > consisting of a matix 384 X 124. > > While using "normailze.quantiles" I find that it introduces 'NA' into some > of the > cells, where we should expect a numerical value, can someone help me to > overcome this problem ? > > The matrix consists of 62 plates in repliccate, and > quantile normailization is done for the data from replicates (colomn 1,2) > using normailze.quantiles function from 'affy' package resulting in data > output as g1 > > >g1 <- normalize.quantiles(exprs(MSExpr[,1:2])) > etc., uptp g62 > > This command works well for smaller series of data, but > while using for a larger data matrix, it introduces "NA" in the place where > it is suppose to geneerate data . It doesn't make any > sense because elsewhere in the colomn consisting of similar values it > computes properly. > > In addition, if I continue to perform median > normailzation of the quantlies, the function fails to > give any output, execept for those colomns which does > not have any "NA". I cannot get rid of interference of NA in median > normalization by using any of NA related functions. > > I am using R in MAC based platform for this analysis. > > Please suggest me some way to avoid 'NA' related computation problem. > Ravi > ravidmurthy at hotmail.com > > _________________________________________________________________ > Dont just search. Find. Check out the new MSN Search! > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor ------------------------------ Message: 6 Date: Fri, 22 Jul 2005 09:04:36 +0000 From: lucia Garc?a <lucia203@hotmail.com> Subject: [BioC] AffyPLM for Windows To: bioconductor at stat.math.ethz.ch Message-ID: <bay103-f523d77a8e41df6f62dc188cc90 at="" phx.gbl=""> Content-Type: text/plain; charset=iso-8859-1; format=flowed Hi, I`m interesting in update AffyPLM to version 1.4.2, but it's only to linux version, but to windows package is 1.3.3. When it will be available the version 1.4.2 for windows? I need this version to fix an error in data of Yeast. This erro will be fixed in affylmGUI? Thanks _________________________________________________________________ Descarga gratis la Barra de Herramientas de MSN ------------------------------ Message: 7 Date: Fri, 22 Jul 2005 11:03:15 +0200 From: "M.A. Bijl" <m.a.bijl@erasmusmc.nl> Subject: [BioC] Spikein Data Package Win32 download problem still present To: bioconductor at stat.math.ethz.ch Message-ID: <42E0B653.8080005 at erasmusmc.nl> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Hi, There is an exact same mailinglist message (dated Mon Jun 20 2005). It's said the problem is fixed, but I guess it isn't. I still can't seem to download the Win32 SpikeIn package from the Experiment Data Packages section (both 1.6 stable and 1.7 devel) : ******start error message****** Access forbidden! You don't have permission to access the requested object. It is either read-protected or not readable by the server. If you think this is a server error, please contact the webmaster <mailto:undefined at="" cobra.fhcrc.org="">. Error 403 www.bioconductor.org <http: www.bioconductor.org=""/> Fri Jul 22 01:43:08 2005 Apache/2.0.49 (Linux/SuSE) ******end error message****** The unix source, again, is fine. If some one could please look into this it would be highly appreciated. Thanks for your attention! Maarten -- B.ICT M.A. Bijl Erasmus MC Dept. of Bioinformatics, Rm. 15.32a/b Dr. Molewaterplein 50 3000 DR Rotterdam The Netherlands TEL: +31 10 40 89381 FAX: +31 10 40 88161 ------------------------------ _______________________________________________ Bioconductor mailing list Bioconductor at stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/bioconductor End of Bioconductor Digest, Vol 29, Issue 21