Thanks Dr.Girke. It worked out. Best Regards, Alex On 6/27/07, Thomas Girke wrote: > > > Alex, > If you post a message on a new topic to this list, then please start a > new email thread instead of replying to an old thread that deals with a > different topic. > > The answer to your question is that the method for accessing the wilcoxon > p-values from mas5calls has been changed with the latest BioConductor > release > 2.0 from > > se.exprs(eset_pma) > > to > > assayDataElement(eset_pma, "se.exprs") > > In the provided example you would type the following: > > my_frame <- data.frame( > exprs(eset_rma), > exprs(eset_pma), > assayDataElement(eset_pma, "se.exprs")) > > I have updated this change now in the exercise code you are referring to. > > Best, > > Thomas > > > > On Tue 06/26/07 21:58, ssls sddd wrote: > > Hi Thomas, > > > > I have another question and need your help. I followed the link > > > http://faculty.ucr.edu/~tgirke/Documents/R_BioCond/R_BioCondManual.html#biocon_limmaaffy > > and tried the code presented in the session of 'BioConductor Exercises'. > > > > I first downloaded 'workshop.zip' file and unpack the files to my > computer. > > I also tired > > six files of my Affy arrays but found the code would not work with *.CEL > > files. I manually > > changed .CEL to .cel and I can play with the code well. > > > > The problem is that when I ran the code: > > > > *my_frame <- data.frame(exprs(eset_rma), exprs(eset_pma), se.exprs > > (eset_pma))* # Combine RMA intensities, P/M/A calls plus their wilcoxon > > p-values in one data frame. > > > > The error message popped up as: > > > > >my_frame <- data.frame(exprs(eset_rma), exprs(eset_pma), > > >se.exprs(eset_pma)) > > > > error in function (classes, fdef, mtable) : > > unable to find an inherited method for function "se.exprs", for > > signature "ExpressionSet" > > > > > > > This also happened for the files from 'workshop.zip'. Can you suggest me > how > > to > > correct this? > > > > > > Thanks a lot! > > > > Sincerely, > > > > Alex > > > > > > On 6/19/07, Thomas Girke wrote: > > > > > >Alex, > > > > > >I guess Martin answered your question. > > > > > >A similar result, but with slower computation, can obtained by applying > > >the IQR function like this: > > > > > > apply(iris[,1:3], 1, IQR) > > > > > >Thomas > > > > > >On Tue 06/19/07 21:10, Martin Morgan wrote: > > >> Alex, > > >> > > >> > library(Biobase) > > >> [snip] > > >> > args(rowQ) > > >> function (imat, which) > > >> NULL > > >> > showMethods("rowQ") > > >> Function: rowQ (package Biobase) > > >> imat="ExpressionSet", which="numeric" > > >> imat="exprSet", which="numeric" > > >> imat="matrix", which="numeric" > > >> > > >> so it looks like x should be a matrix rather than a data frame. > > >> > > >> Martin > > >> > > >> "ssls sddd" writes: > > >> > > >> > Hi Thomas, > > >> > > > >> > Thanks! Sorry for getting back to it late because I was out > > >> > of town for a couple of days. > > >> > > > >> > I like the idea of 'removing all rows with low variability across > > >> > samples'. I searched around and found an online tutorial > > >> > > > > > http://www.economia.unimi.it/projects/marray/2006/material/Lab3/MachineLearning/ML-lab.pdfis > > >> > doing very similar thing which teaches how to filter some > > >> > undifferentially > > >> > expressed genes. > > >> > > > >> > It takes the simplistic approach of using the 75th percentile of > the > > >> > interquartile range > > >> > (IQR) as the cut-off point and computes quantiles using rowQ. > > >> > > > >> > I followed their method and my code is: > > >> > > > >> > library("Biobase") > > >> > lowQ = rowQ(x, floor(0.25 * 49))#49 for 49 samples > > >> > upQ = rowQ(x, ceiling(0.75 * 49)) > > >> > iqrs = upQ - lowQ > > >> > giqr = iqrs > quantile(iqrs, probs = 0.75) > > >> > sum(giqr) > > >> > xsub = x[giqr, ] > > >> > dim(xsub) > > >> > > > >> > But the error message is like: > > >> > > > >> > function (classes, fdef, mtable) : > > >> > unable to find an inherited method for function "rowQ", for > > >> > signature "data.frame", "numeric" > > >> > > > >> > Perhaps you can any experience in using 'rowQ'? If I want to use > IQR > > >> > function, how should I approach this? > > >> > > > >> > I really appreciate your help! > > >> > > > >> > Thank you very much! > > >> > > > >> > Sincerely, > > >> > > > >> > Alex > > >> > > > >> > > > >> > > > >> > On 6/13/07, Thomas Girke wrote: > > >> >> > > >> >> Dear Alex, > > >> >> > > >> >> In addition, to Sean's advice, I would like to point out that the > > >> >> sample you are giving below indicates that you are trying to pass > on > > >> >> to the heatmap function a column dendrogram plus a row dendrogram. > > >With > > >> >> your > > >> >> matrix of 238,000 rows by 49 columns you should have only a column > > >> >> dendrogram, because the row dendrogram would take more than 200 GB > of > > >> >> memory to > > >> >> calculate. You can still use the heatmap or heatmap.2 functions by > > >turning > > >> >> off the row > > >> >> sorting by setting the Rowv argument to NA. In addition to this, I > > >would > > >> >> consider to filter your rows in a meaningful manner to a much > smaller > > >> >> number, perhaps by using R's IQR function to remove all rows with > > >very > > >> >> low variability. I am suggesting this because, you won't see any > > >> >> patterns in the heatmap when you have so many rows. If the row > > >filtering > > >> >> works then you could generate a dendrogram for the row dimension > as > > >well. > > >> >> Remember: hclust will require ~4 GB of memory to cluster ~30,000 > > >items > > >> >> and < 1 GB for 10,000 items, and pvclust that uses hclust > internally > > >will > > >> >> need even much more than this. > > >> >> > > >> >> As a more general advice, when working with large data sets in R > > >always > > >> >> subset > > >> >> your data to something very small to test out your strategy first, > > >because > > >> >> this > > >> >> will save you a lot of time. > > >> >> In your case, this could by done by selecting just the first 100 > rows > > >of > > >> >> your > > >> >> matrix like this: > > >> >> my_matrix <- my_matrix[1:100, ] > > >> >> > > >> >> Once you have tested things out then just remove in your > > >script/protocol > > >> >> the '[1:100,]' part. > > >> >> > > >> >> Best, > > >> >> > > >> >> Thomas > > >> >> > > >> >> > > >> >> On Wed 06/13/07 06:02, Sean Davis wrote: > > >> >> > ssls sddd wrote: > > >> >> > > Dear Dr.Thomas Girke, > > >> >> > > > > >> >> > > I have one more question for you. I tried pvclust in the > session > > >of > > >> >> > > 'Obtain significant clusters by pvclust bootstrap analysis' > for > > >my > > >> >> data, x. > > >> >> > > > > >> >> > > But I have a problem with: > > >> >> > > > > >> >> > > heatmap(x, Rowv=dend_colored, Colv=as.dendrogram(hc), col= > > >my.colorFct > > >> >> (), > > >> >> > > scale="row", RowSideColors=mycolhc) > > >> >> > > > > >> >> > > the error was: > > >> >> > > > > >> >> > > error in heatmap(x, Rowv = dend_colored, Colv = as.dendrogram > (hc), > > >col > > >> >> = > > >> >> > > my.colorFct(), : > > >> >> > > 'x' must be a numeric matrix > > >> >> > > > > >> >> > > I ran 'x[1:3,1:3]' and it produced the following: > > >> >> > > > > >> >> > > AIRNS_A09 AIRNS_A11 AIRNS_A12 > > >> >> > > SNP_A-1780271 1.85642 1.50956 1.73154 > > >> >> > > SNP_A-1780274 1.72140 1.83712 1.85948 > > >> >> > > SNP_A-1780277 2.04241 1.53458 1.65270 > > >> >> > > > > >> >> > > I think the x is a numeric matrix. Do you think where I may > get > > >wrong? > > >> >> > > > >> >> > Try coercing the x into a matrix directly: > > >> >> > > > >> >> > heatmap(as.matrix(x), Rowv=dend_colored, Colv=as.dendrogram(hc), > > >> >> > col=my.colorFct(), scale="row", RowSideColors=mycolhc) > > >> >> > > > >> >> > Does this fix the problem? You can always check the class of an > > >object > > >> >> > by doing something like: > > >> >> > > > >> >> > class(x) > > >> >> > > > >> >> > which should report: > > >> >> > > > >> >> > [1] "matrix" > > >> >> > > > >> >> > Hope that helps. > > >> >> > > > >> >> > Sean > > >> >> > > > >> >> > > >> >> -- > > >> >> Dr. Thomas Girke > > >> >> Assistant Professor of Bioinformatics > > >> >> Director, IIGB Bioinformatic Facility > > >> >> Center for Plant Cell Biology (CEPCEB) > > >> >> Institute for Integrative Genome Biology (IIGB) > > >> >> Department of Botany and Plant Sciences > > >> >> 1008 Noel T. Keen Hall > > >> >> University of California > > >> >> Riverside, CA 92521 > > >> >> > > >> >> E-mail: thomas.girke@ucr.edu > > >> >> Website: http://faculty.ucr.edu/~tgirke < > > >http://faculty.ucr.edu/%7Etgirke> > > >> >> Ph: 951-827-2469 > > >> >> Fax: 951-827-4437 > > >> >> > > >> > > > >> > [[alternative HTML version deleted]] > > >> > > > >> > _______________________________________________ > > >> > Bioconductor mailing list > > >> > Bioconductor@stat.math.ethz.ch > > >> > https://stat.ethz.ch/mailman/listinfo/bioconductor > > >> > Search the archives: > > >http://news.gmane.org/gmane.science.biology.informatics.conductor > > >> > > >> -- > > >> Martin Morgan > > >> Bioconductor / Computational Biology > > >> http://bioconductor.org > > >> > > >> _______________________________________________ > > >> Bioconductor mailing list > > >> Bioconductor@stat.math.ethz.ch > > >> https://stat.ethz.ch/mailman/listinfo/bioconductor > > >> Search the archives: > > >http://news.gmane.org/gmane.science.biology.informatics.conductor > > >> > > > > > >-- > > >Thomas Girke > > >Assistant Professor of Bioinformatics > > >Director, IIGB Bioinformatic Facility > > >Center for Plant Cell Biology (CEPCEB) > > >Institute for Integrative Genome Biology (IIGB) > > >Department of Botany and Plant Sciences > > >1008 Noel T. Keen Hall > > >University of California > > >Riverside, CA 92521 > > > > > >E-mail: thomas.girke@ucr.edu > > >Website: http://faculty.ucr.edu/~tgirke > > >Ph: 951-827-2469 > > >Fax: 951-827-4437 > > > > > -- > Thomas Girke > Assistant Professor of Bioinformatics > Director, IIGB Bioinformatic Facility > Center for Plant Cell Biology (CEPCEB) > Institute for Integrative Genome Biology (IIGB) > Department of Botany and Plant Sciences > 1008 Noel T. Keen Hall > University of California > Riverside, CA 92521 > > E-mail: thomas.girke@ucr.edu > Website: http://faculty.ucr.edu/~tgirke > Ph: 951-827-2469 > Fax: 951-827-4437 > [[alternative HTML version deleted]]