#### The support.bioconductor.org editor has been updated to markdown! Please see more info at: Tutorial: Updated Support Site Editor

Question: class label
0
8.2 years ago by
Peevi Ijkl170
Peevi Ijkl170 wrote:
Hello ok my phenodata(target.txt) looks something like this 1.CEL A 1.CEL A 3.CEL A 4.CEL H 5.CEL H 6.CEL H i loaded the above into my R using library(affy) library(simpleaffy) eset<-read.AnnotatedDataFrame("target.txt", header=T, row.names=1, sep="\t" ) to view my data: pData(eset) then i did normalization on it Rmaeset<-rma(eset) now i want to perform multtest..but first i have to create class label..can anyone tell me how do i do tht?? peevi [[alternative HTML version deleted]]
normalization multtest • 456 views
modified 8.2 years ago by Martin Morgan ♦♦ 22k • written 8.2 years ago by Peevi Ijkl170
0
8.2 years ago by
Martin Morgan ♦♦ 22k
United States
Martin Morgan ♦♦ 22k wrote:
On 12/18/2010 07:56 AM, Peevi Ijkl wrote: > Hello > ok my phenodata(target.txt) looks something like this > > 1.CEL A > 1.CEL A > 3.CEL A > 4.CEL H > 5.CEL H > 6.CEL H > > i loaded the above into my R using > library(affy) > library(simpleaffy) > eset<-read.AnnotatedDataFrame("target.txt", header=T, row.names=1, sep="\t" ) > > to view my data: > pData(eset) > > then i did normalization on it > > Rmaeset<-rma(eset) > > now i want to perform multtest..but first i have to create class label..can > anyone tell me how do i do tht?? Hi peevi -- You need to be more helpful to us, and stick with your original question. Likely the problem is that your pd$Diabetic variable is not what you think it is, e.g., a factor when you're expecting it to be a character, or of the wrong length, or ???. But how are we to know? You have to show it to us. And you can't really say 'multtest doesn't work', because we know that example(multtest) *does* work. And since even simple emails like this can take five minutes to write, you have to make it easy for us to see what your problem might be, so no sense giving us a dozen lines of code -- reduce your real problem to something that shows what the issue is, in just a few lines, and nothing more. Martin > > peevi > > > > > [[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 -- Computational Biology Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: M1-B861 Telephone: 206 667-2793 ADD COMMENTlink written 8.2 years ago by Martin Morgan ♦♦ 22k Hello martin i know that multtest works..but for it to work correctly i need to create a class label right..which am not able to ..i am attching the original txt file that i created..it is tab delimited.. ID disease GSM469509.CEL A GSM469510.CEL A GSM469511.CEL A GSM469512.CEL A GSM469514.CEL A GSM469518.CEL A GSM469520.CEL A GSM469522.CEL A GSM469523.CEL A GSM469508.CEL H GSM469513.CEL H GSM469515.CEL H GSM469516.CEL H GSM469517.CEL H GSM469519.CEL H GSM469521.CEL H A stands for atopic,H for healthy normal now i want to create a class label..can u help? peevi ________________________________ From: Martin Morgan <mtmorgan@fhcrc.org> Cc: bioconductor <bioconductor@stat.math.ethz.ch> Sent: Sat, December 18, 2010 11:02:23 AM Subject: Re: [BioC] class label On 12/18/2010 07:56 AM, Peevi Ijkl wrote: > Hello > ok my phenodata(target.txt) looks something like this > > 1.CEL A > 1.CEL A > 3.CEL A > 4.CEL H > 5.CEL H > 6.CEL H > > i loaded the above into my R using > library(affy) > library(simpleaffy) > eset<-read.AnnotatedDataFrame("target.txt", header=T, row.names=1, sep="\t" ) > > to view my data: > pData(eset) > > then i did normalization on it > > Rmaeset<-rma(eset) > > now i want to perform multtest..but first i have to create class label..can > anyone tell me how do i do tht?? Hi peevi -- You need to be more helpful to us, and stick with your original question. Likely the problem is that your pd$Diabetic variable is not what you think it is, e.g., a factor when you're expecting it to be a character, or of the wrong length, or ???. But how are we to know? You have to show it to us. And you can't really say 'multtest doesn't work', because we know that example(multtest) *does* work. And since even simple emails like this can take five minutes to write, you have to make it easy for us to see what your problem might be, so no sense giving us a dozen lines of code -- reduce your real problem to something that shows what the issue is, in just a few lines, and nothing more. Martin > > peevi > > > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: >http://news.gmane.org/gmane.science.biology.informatics.conductor -- Computational Biology Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: M1-B861 Telephone: 206 667-2793 [[alternative HTML version deleted]]
On 12/18/2010 09:45 AM, Peevi Ijkl wrote: > Hello martin > i know that multtest works..but for it to work correctly i need to > create a class label right..which am not able to ..i am attching the > original txt file that i created..it is tab delimited.. > ID disease > GSM469509.CEL A > GSM469510.CEL A > GSM469511.CEL A > GSM469512.CEL A > GSM469514.CEL A > GSM469518.CEL A > GSM469520.CEL A > GSM469522.CEL A > GSM469523.CEL A > GSM469508.CEL H > GSM469513.CEL H > GSM469515.CEL H > GSM469516.CEL H > GSM469517.CEL H > GSM469519.CEL H > GSM469521.CEL H > A stands for atopic,H for healthy normal > now i want to create a class label..can u help? Hi peevi -- I know you're trying, and in some ways I'm being less helpful than I could be. But this isn't helpful -- attachments are removed by the mailing list software, you could have read this data in through several different ways (especially stringsAsFactors=TRUE or FALSE could be important), it doesn't relate to your original question (there is no column 'Diabetic', and no variable that it would seem reasonable to compare to "y") and we don't know what function you are trying to use or from which library it is supposed to come from. To return to my previous suggestion, here's what I'd guess, cut and pasted from my R session > library(multtest) > lbl <- pd$Diabetic > m <- matrix(runif(10 * length(pd$Diabetic)), 10) > str(lbl) Factor w/ 2 levels "n","y": 2 2 2 2 1 1 1 1 > res <- mt.teststat(m, as.integer(lbl=="y")) but what do you actually do and see? It could also be that you are using an older version of software (though I doubt that's the case here) and so we encourage (a) making sure that you are using current software by following the instructions to update packages at http://localhost:3000/install/index.html#update-bioconductor- packages and (b) providing the output of sessionInfo() after the error has occurred, and in an R session that is used only to provide the minimal example. Here's mine > sessionInfo() R version 2.12.0 Patched (2010-11-21 r53647) Platform: x86_64-unknown-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] multtest_2.6.0 Biobase_2.10.0 loaded via a namespace (and not attached): [1] MASS_7.3-9 splines_2.12.0 survival_2.36-2 tools_2.12.0 Martin > > peevi > > > -------------------------------------------------------------------- ---- > *From:* Martin Morgan <mtmorgan at="" fhcrc.org=""> > *To:* Peevi Ijkl <ipeevi at="" yahoo.com=""> > *Cc:* bioconductor <bioconductor at="" stat.math.ethz.ch=""> > *Sent:* Sat, December 18, 2010 11:02:23 AM > *Subject:* Re: [BioC] class label > > On 12/18/2010 07:56 AM, Peevi Ijkl wrote: >> Hello >> ok my phenodata(target.txt) looks something like this >> >> 1.CEL A >> 1.CEL A >> 3.CEL A >> 4.CEL H >> 5.CEL H >> 6.CEL H >> >> i loaded the above into my R using >> library(affy) >> library(simpleaffy) >> eset<-read.AnnotatedDataFrame("target.txt", header=T, row.names=1, > sep="\t" ) >> >> to view my data: >> pData(eset) >> >> then i did normalization on it >> >> Rmaeset<-rma(eset) >> >> now i want to perform multtest..but first i have to create class > label..can >> anyone tell me how do i do tht?? > > Hi peevi -- You need to be more helpful to us, and stick with your > original question. Likely the problem is that your pd\$Diabetic variable > is not what you think it is, e.g., a factor when you're expecting it to > be a character, or of the wrong length, or ???. But how are we to know? > You have to show it to us. And you can't really say 'multtest doesn't > work', because we know that > > example(multtest) > > *does* work. And since even simple emails like this can take five > minutes to write, you have to make it easy for us to see what your > problem might be, so no sense giving us a dozen lines of code -- reduce > your real problem to something that shows what the issue is, in just a > few lines, and nothing more. > > > Martin > >> >> peevi >> >> >> >> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at r-project.org <mailto:bioconductor at="" r-project.org=""> >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > > > -- > Computational Biology > Fred Hutchinson Cancer Research Center > 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 > > Location: M1-B861 > Telephone: 206 667-2793 > -- Computational Biology Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: M1-B861 Telephone: 206 667-2793