help with multtest and annaffy
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@taylor-katie-4048
Last seen 8.1 years ago
Hi, I have followed the annaffy vignette online and successfully created the HTML documents for annotating the aafExpr dataset. When I try to do the same with my data (GDS2609) which I downloaded from GEO I can only get so far and then R becomes unresponsive and is forced to close. I have copied the session info below: 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > library(affy); library(limma) Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material. To view, type 'openVignette()'. To cite Bioconductor, see 'citation("Biobase")' and for packages 'citation(pkgname)'. > Data <- ReadAffy() > Gds2609 <- Data > eset <- rma(Gds2609) Background correcting Normalizing Calculating Expression > pData(eset) sample GSM93789.CEL 1 GSM93920.CEL 2 GSM93952.CEL 3 GSM93954.CEL 4 > strain <- c("n", "n", "c", "c") > design <- model.matrix(~factor(strain)) > colnames(design) <- c("n", "c") > design n c 1 1 1 2 1 1 3 1 0 4 1 0 attr(,"assign") [1] 0 1 attr(,"contrasts") attr(,"contrasts")$factor(strain) [1] "contr.treatment" library(multtest) > class <- as.integer(pData(Gds2609)$covar1) - 1 > teststat <- mt.teststat(exprs(Gds2609), class) ##at this point R is forced to close each time I try it. > sessionInfo() ## had to do this command before teststat otherwise R closes before I can do it R version 2.11.0 (2010-04-22) i386-pc-mingw32 locale: [1] LC_COLLATE=English_United Kingdom.1252 [2] LC_CTYPE=English_United Kingdom.1252 [3] LC_MONETARY=English_United Kingdom.1252 [4] LC_NUMERIC=C [5] LC_TIME=English_United Kingdom.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] multtest_2.4.0 hgu133plus2cdf_2.6.0 limma_3.4.0 [4] affy_1.26.0 Biobase_2.8.0 loaded via a namespace (and not attached): [1] affyio_1.16.0 MASS_7.3-5 preprocessCore_1.10.0 [4] splines_2.11.0 survival_2.35-8 tools_2.11.0 > The commands that I want to use after this are as follows: index <- order(abs(teststat), decreasing = TRUE) probeids <- featureNames(Gds2609)[index] library(annaffy) aaf.handler() anncols <- aaf.handler()[c(1:3, 8:9, 11:13)] anntable <- aafTableAnn(probeids[1:250], "hgu133plus2.db", anncols) saveHTML(anntable, "example1.html", title = "Example Table without Data") testtable <- aafTable(t-statistic = teststat[index[1:250]], signed = TRUE) table <- merge(anntable, testtable) exprtable <- aafTableInt(Gds2609, probeids = probeids[1:250]) table <- merge(table, exprtable) saveHTML(table, "example2.html", title = "Example Table with Data") saveText(table, "example2.txt") If anyone has any ideas why R keeps closing on me like this I would really appreciate your help. I've tried running R on different computers as I didn't know if it was a memory problem but the example in the annaffy pdf works fine. I have no idea what is happening and could really do with some help. Best Wishes, Katie
annaffy annaffy • 669 views
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@james-w-macdonald-5106
Last seen 13 hours ago
United States
Hi Katie, Taylor, Katie wrote: > Hi, > > I have followed the annaffy vignette online and successfully created the HTML documents for annotating the aafExpr dataset. When I try to do the same with my data (GDS2609) which I downloaded from GEO I can only get so far and then R becomes unresponsive and is forced to close. I have copied the session info below: > > 'help.start()' for an HTML browser interface to help. > Type 'q()' to quit R. > >> library(affy); library(limma) > Loading required package: Biobase > > Welcome to Bioconductor > > Vignettes contain introductory material. To view, type > 'openVignette()'. To cite Bioconductor, see > 'citation("Biobase")' and for packages 'citation(pkgname)'. > >> Data <- ReadAffy() >> Gds2609 <- Data >> eset <- rma(Gds2609) > Background correcting > Normalizing > Calculating Expression >> pData(eset) > sample > GSM93789.CEL 1 > GSM93920.CEL 2 > GSM93952.CEL 3 > GSM93954.CEL 4 >> strain <- c("n", "n", "c", "c") >> design <- model.matrix(~factor(strain)) >> colnames(design) <- c("n", "c") >> design > n c > 1 1 1 > 2 1 1 > 3 1 0 > 4 1 0 > attr(,"assign") > [1] 0 1 > attr(,"contrasts") > attr(,"contrasts")$factor(strain) > [1] "contr.treatment" Unless you are using limma, the above (after pData(eset)) is superfluous. > library(multtest) >> class <- as.integer(pData(Gds2609)$covar1) - 1 As Sean Davis mentioned the last time you asked, class isn't a very good name, as it is also a function name. Using something like classlabel instead is a more reasonable approach. In addition, you might show what is in this vector. In addition, it looks like you are getting mixed up in all your gyrations above (why call the AffyBatch 'Data' and then immediately copy it into another AffyBatch called Gds2609? You are just chewing up RAM unnecessarily.). The 'Gds2609' object is an AffyBatch, not an ExpressionSet. Although exprs() will work on an AffyBatch, the matrix you are outputting is over ten times the size of the matrix that I think you want (exprs(eset)). Best, Jim >> teststat <- mt.teststat(exprs(Gds2609), class) ##at this point R is forced to close each time I try it. >> sessionInfo() ## had to do this command before teststat otherwise R closes before I can do it > R version 2.11.0 (2010-04-22) > i386-pc-mingw32 > > locale: > [1] LC_COLLATE=English_United Kingdom.1252 > [2] LC_CTYPE=English_United Kingdom.1252 > [3] LC_MONETARY=English_United Kingdom.1252 > [4] LC_NUMERIC=C > [5] LC_TIME=English_United Kingdom.1252 > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] multtest_2.4.0 hgu133plus2cdf_2.6.0 limma_3.4.0 > [4] affy_1.26.0 Biobase_2.8.0 > > loaded via a namespace (and not attached): > [1] affyio_1.16.0 MASS_7.3-5 preprocessCore_1.10.0 > [4] splines_2.11.0 survival_2.35-8 tools_2.11.0 > > > The commands that I want to use after this are as follows: > index <- order(abs(teststat), decreasing = TRUE) > probeids <- featureNames(Gds2609)[index] > library(annaffy) > aaf.handler() > anncols <- aaf.handler()[c(1:3, 8:9, 11:13)] > anntable <- aafTableAnn(probeids[1:250], "hgu133plus2.db", anncols) > saveHTML(anntable, "example1.html", title = "Example Table without Data") > testtable <- aafTable(t-statistic = teststat[index[1:250]], > signed = TRUE) > table <- merge(anntable, testtable) > exprtable <- aafTableInt(Gds2609, probeids = probeids[1:250]) > table <- merge(table, exprtable) > saveHTML(table, "example2.html", title = "Example Table with Data") > saveText(table, "example2.txt") > > > If anyone has any ideas why R keeps closing on me like this I would really appreciate your help. I've tried running R on different computers as I didn't know if it was a memory problem but the example in the annaffy pdf works fine. I have no idea what is happening and could really do with some help. > > Best Wishes, > > Katie > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- James W. MacDonald, M.S. Biostatistician Douglas Lab University of Michigan Department of Human Genetics 5912 Buhl 1241 E. Catherine St. Ann Arbor MI 48109-5618 734-615-7826 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues