"I am facing a problem in microarray gene expression analysis. I have uploaded a simple normalized text data file (i.e. of just 1.5Mb), Here is the sample of my dataset used. Dis1 Dis2 Dis3 Dis4 Nor1 Nor2 Nor3 Gene1 0 0.087 0 0 0 0 0.157 Gene2 1.847 0.74 1.571 1.346 0.339 0.6 0.996 Gene3 0.041 0.161 1.338 0.293 0 0.553 0.122 Gene4 17.542 12.585 10.273 10.927 6.128 12.842 12.663 Gene5 0.332 0.038 0.347 0.091 0.064 0 0.233 Gene6 0.975 0.333 0.34 0.711 0.497 0.446 0.557 as my data is already is normalized one thus straightaway I wish to simply apply t-statistics, when i clicked on "T-statistics" section and in order to find differentially expressed genes I have opted two classes in one dataset, and set p value as 0.05 and for correction Benjamin-Hochberg. But instead of displaying result it shows the following error. R: Loading required package: tools Welcome to Bioconductor Vignettes contain introductory material. To view, type 'openVignette()' or start with 'help(Biobase)'. For details on reading vignettes, see the openVignette help page. Hmisc library by Frank E Harrell Jr Type library(help='Hmisc'), ?Overview, or ?Hmisc.Overview') to see overall documentation. NOTE:Hmisc no longer redefines [.factor to drop unused levels when subsetting. To get the old behavior of Hmisc type dropUnusedLevels(). Attaching package: 'Hmisc' The following object(s) are masked from package:Biobase : contents Error in plot.window(xlim, ylim, log, asp, ...) : need finite 'xlim' values KINDLY HELP ME TO SOLVE THE ISSUE. I WILL BE VERY GREATFUL TO YOU THANKYOU" [[alternative HTML version deleted]]

Hi, As Marco has already mentioned: it's not clear what software you are using. It seems as if you have a rather straightforward experimental design (testing differential expression between two conditions, each of which has several replicates). Since you posted on the bioconductor mailing list, I'm going to assume that you want to use bioconductor tools to solve your problem. If I were you, I'd use limma: http://www.bioconductor.org/packages/release/bioc/html/limma.html Read through the user guide: http://www.bioconductor.org/packages/release/bioc/vignettes/limma/inst /doc/usersguide.pdf Pay attention to the case study section. You'll likely find something quite similar to your setup in there. Also: DON'T TYPE IN CAPS, IT WILL MORE LIKELY ANGER PEOPLE THAN ENCOURAGE THEM TO HELP YOU BECAUSE YOU ARE COMING OFF AS DEMANDING SOMETHING, EVEN THOUGH YOU PROBABLY DON'T INTEND TO. Good luck, -steve On Fri, Feb 25, 2011 at 5:49 AM, Poonam ** <vpoonam89 at="" gmail.com=""> wrote: > "I am facing a problem in microarray gene expression analysis. I have > uploaded a simple normalized text data file (i.e. of just 1.5Mb), > Here is the sample of my dataset used. > > ? ? ? Dis1 ? ?Dis2 ? ?Dis3 ? ?Dis4 ? ?Nor1 ? ?Nor2 ? ?Nor3 > Gene1 ? 0 ? ? ? 0.087 ? 0 ? ? ? 0 ? ? ? 0 ? ? ? 0 ? ? ? 0.157 > Gene2 ? 1.847 ? 0.74 ? ?1.571 ? 1.346 ? 0.339 ? 0.6 ? ? 0.996 > Gene3 ? 0.041 ? 0.161 ? 1.338 ? 0.293 ? 0 ? ? ? 0.553 ? 0.122 > Gene4 ? 17.542 ?12.585 ?10.273 ?10.927 ?6.128 ? 12.842 ?12.663 > Gene5 ? 0.332 ? 0.038 ? 0.347 ? 0.091 ? 0.064 ? 0 ? ? ? 0.233 > Gene6 ? 0.975 ? 0.333 ? 0.34 ? ?0.711 ? 0.497 ? 0.446 ? 0.557 > > > ?as my data is already is normalized one thus straightaway I wish to simply > apply t-statistics, when i clicked on "T-statistics" section and in order to > find differentially expressed genes I have opted two classes in one dataset, > and set p value as 0.05 and for correction Benjamin-Hochberg. > > > But instead of displaying result it shows the following error. > R: Loading required package: tools > Welcome to Bioconductor > Vignettes contain introductory material. To view, type > 'openVignette()' or start with 'help(Biobase)'. For details > on reading vignettes, see the openVignette help page. > Hmisc library by Frank E Harrell Jr > Type library(help='Hmisc'), ?Overview, or ?Hmisc.Overview') > to see overall documentation. > NOTE:Hmisc no longer redefines [.factor to drop unused levels when > subsetting. To get the old behavior of Hmisc type dropUnusedLevels(). > Attaching package: 'Hmisc' > The following object(s) are masked from package:Biobase : > contents > Error in plot.window(xlim, ylim, log, asp, ...) : > need finite 'xlim' values > > > KINDLY HELP ME TO SOLVE THE ISSUE. I WILL BE VERY GREATFUL TO YOU > THANKYOU" > > ? ? ? ?[[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > -- Steve Lianoglou Graduate Student: Computational Systems Biology ?| Memorial Sloan-Kettering Cancer Center ?| Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact

Also -- I just realized this (since I got a bounce back), but please don't CC bioconductor-request at r-project.org in your emails. By default, people reply to emails via reply-all, so we're all stuck sending emails there too, if we're not careful enough to notice that the "request" email address is in there. Please just send your bioc questions to: bioconductor at r-project.org Thanks, -steve On Fri, Feb 25, 2011 at 5:49 AM, Poonam ** <vpoonam89 at="" gmail.com=""> wrote: > "I am facing a problem in microarray gene expression analysis. I have > uploaded a simple normalized text data file (i.e. of just 1.5Mb), > Here is the sample of my dataset used. > > ? ? ? Dis1 ? ?Dis2 ? ?Dis3 ? ?Dis4 ? ?Nor1 ? ?Nor2 ? ?Nor3 > Gene1 ? 0 ? ? ? 0.087 ? 0 ? ? ? 0 ? ? ? 0 ? ? ? 0 ? ? ? 0.157 > Gene2 ? 1.847 ? 0.74 ? ?1.571 ? 1.346 ? 0.339 ? 0.6 ? ? 0.996 > Gene3 ? 0.041 ? 0.161 ? 1.338 ? 0.293 ? 0 ? ? ? 0.553 ? 0.122 > Gene4 ? 17.542 ?12.585 ?10.273 ?10.927 ?6.128 ? 12.842 ?12.663 > Gene5 ? 0.332 ? 0.038 ? 0.347 ? 0.091 ? 0.064 ? 0 ? ? ? 0.233 > Gene6 ? 0.975 ? 0.333 ? 0.34 ? ?0.711 ? 0.497 ? 0.446 ? 0.557 > > > ?as my data is already is normalized one thus straightaway I wish to simply > apply t-statistics, when i clicked on "T-statistics" section and in order to > find differentially expressed genes I have opted two classes in one dataset, > and set p value as 0.05 and for correction Benjamin-Hochberg. > > > But instead of displaying result it shows the following error. > R: Loading required package: tools > Welcome to Bioconductor > Vignettes contain introductory material. To view, type > 'openVignette()' or start with 'help(Biobase)'. For details > on reading vignettes, see the openVignette help page. > Hmisc library by Frank E Harrell Jr > Type library(help='Hmisc'), ?Overview, or ?Hmisc.Overview') > to see overall documentation. > NOTE:Hmisc no longer redefines [.factor to drop unused levels when > subsetting. To get the old behavior of Hmisc type dropUnusedLevels(). > Attaching package: 'Hmisc' > The following object(s) are masked from package:Biobase : > contents > Error in plot.window(xlim, ylim, log, asp, ...) : > need finite 'xlim' values > > > KINDLY HELP ME TO SOLVE THE ISSUE. I WILL BE VERY GREATFUL TO YOU > THANKYOU" > > ? ? ? ?[[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > -- Steve Lianoglou Graduate Student: Computational Systems Biology ?| Memorial Sloan-Kettering Cancer Center ?| Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact

Dear Poonam, first of all might I invite you to read the posting guide here? -> http://www.bioconductor.org/help/mailing-list/posting-guide/ Might I also remind you that is commonly accepted netiquette not to use afinalistic text capitalization in a message, as it is equivalent to screaming to try to catch someone's attention in real world? That said, I am not sure what kind of software environment are you working on when you mention << i clicked on "T-statistics" section>>. Could you give us some background on the installation of R/Bioconductor you are working on? On which OS? Could you copy and paste the code you are using, either by writing it yourself or by mean of an intermediate interface, and the results of your sessionInfo() and traceback()? If you are using a proprietary software which is in turn summoning R, maybe it could be relevant to contact their assistance service. All the best, Marco -- Marco Manca, MD University of Maastricht Faculty of Health, Medicine and Life Sciences (FHML) Cardiovascular Research Institute (CARIM) Mailing address: PO Box 616, 6200 MD Maastricht (The Netherlands) Visiting address: Experimental Vascular Pathology group, Dept of Pathology - Room5.08, Maastricht University Medical Center, P. Debyelaan 25, 6229 HX Maastricht E-mail: m.manca at maastrichtuniversity.nl Office telephone: +31(0)433874633 Personal mobile: +31(0)626441205 Twitter: @markomanka ********************************************************************** *********************************************** This email and any files transmitted with it are confidential and solely for the use of the intended recipient. It may contain material protected by privacy or attorney-client privilege. If you are not the intended recipient or the person responsible for delivering to the intended recipient, be advised that you have received this email in error and that any use is STRICTLY PROHIBITED. If you have received this email in error please notify us by telephone on +31626441205 Dr Marco MANCA ********************************************************************** *********************************************** ________________________________________ Da: bioconductor-bounces at r-project.org [bioconductor-bounces at r-project.org] per conto di Poonam ** [vpoonam89 at gmail.com] Inviato: venerd? 25 febbraio 2011 11.49 A: bioconductor-request at r-project.org; bioconductor at r-project.org Oggetto: [BioC] HELP: MICROARRAYS "I am facing a problem in microarray gene expression analysis. I have uploaded a simple normalized text data file (i.e. of just 1.5Mb), Here is the sample of my dataset used. Dis1 Dis2 Dis3 Dis4 Nor1 Nor2 Nor3 Gene1 0 0.087 0 0 0 0 0.157 Gene2 1.847 0.74 1.571 1.346 0.339 0.6 0.996 Gene3 0.041 0.161 1.338 0.293 0 0.553 0.122 Gene4 17.542 12.585 10.273 10.927 6.128 12.842 12.663 Gene5 0.332 0.038 0.347 0.091 0.064 0 0.233 Gene6 0.975 0.333 0.34 0.711 0.497 0.446 0.557 as my data is already is normalized one thus straightaway I wish to simply apply t-statistics, when i clicked on "T-statistics" section and in order to find differentially expressed genes I have opted two classes in one dataset, and set p value as 0.05 and for correction Benjamin-Hochberg. But instead of displaying result it shows the following error. R: Loading required package: tools Welcome to Bioconductor Vignettes contain introductory material. To view, type 'openVignette()' or start with 'help(Biobase)'. For details on reading vignettes, see the openVignette help page. Hmisc library by Frank E Harrell Jr Type library(help='Hmisc'), ?Overview, or ?Hmisc.Overview') to see overall documentation. NOTE:Hmisc no longer redefines [.factor to drop unused levels when subsetting. To get the old behavior of Hmisc type dropUnusedLevels(). Attaching package: 'Hmisc' The following object(s) are masked from package:Biobase : contents Error in plot.window(xlim, ylim, log, asp, ...) : need finite 'xlim' values KINDLY HELP ME TO SOLVE THE ISSUE. I WILL BE VERY GREATFUL TO YOU THANKYOU" [[alternative HTML version deleted]] _______________________________________________ Bioconductor mailing list Bioconductor at r-project.org https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor