[R] illumina array - remove probes in discontinued genes
Hi I'm working with the illumina HT-12v4 array and after using LIMMA some of the most significant probes that come up are in genes that have been discontinued on NCBI (ie LOC732450). Is there a way to filter my data of these probes prior to statisitcal analysis? Thanks, .kripa [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] illumina probeID to entrezID
Hi, how do you convert the illumina ProbeID to entrezID? I've used LIMMA to identify top genes but i'm not sure how to apply illuminaHumanv4.db to get the EntrezID. Thanks in advance, .kripa [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] GLMNET warning msg
Hi I'm getting the following warning msg after ?cv.glmnet and I'm wondering what it means... dim(x) 10 12000; dim(y) 10; #two groups case=1 and control=0 cv.glmnet(x, y) Warning message: Option grouped=FALSE enforced in cv.glmnet, since 3 observations per fold Thanks, .kripa [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] PAMR - adding additional labels
Hello, I recently started using PAM to analyze my microarrays (http://cran.r-project.org/web/packages/pamr/pamr.pdf). Firstly does anyone know of a specific forum or help section for this package? Currently with ?pamr.from.excel you can only have one line of labels, ie control vs treatment. But I'd like to add additional variables such as bmi, does anyone know if this is possible? Or would it be better to residualize my data set for confounders (such as bmi) and then put it through PAM? Thanks in advance, .kripa [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] pulling out pairs from data frame
Oops! Ok So I have this file: SampleName Individual Age Gender 1 4 80 M 2 15 56 F 3 1 75 F 4 15 56 F 5 2 58 F 6 4 80 M And I want to pull out paired samples, so the resulting file would look something like this: SampleName Individual Age Gender 1 4 80 M 2 15 56 F 4 15 56 F 6 4 80 M .kripa Date: Mon, 12 Aug 2013 18:36:08 -0700 From: smartpink...@yahoo.com Subject: Re: [R] pulling out pairs from data frame To: kripa...@hotmail.com CC: r-help@r-project.org Hi, The question is not clear so not sure this is what you wanted. dat1- read.table(text= SameName áIndividual áAge Gender 1 4 á80 áM á 2 15 á56 F 3 1 75 áF 4 15 á56 áF 5 á2 á58 áF 6 4 á80 áM ,sep=,header=TRUE,stringsAsFactors=FALSE) reps-c(4,15)á ádat1$Newcol-as.numeric(dat1$Individual%in% reps) ádat1 # áSameName Individual Age Gender Newcol #1 á á á á1 á á á á á4 á80 á á áM á á á1 #2 á á á á2 á á á á 15 á56 á á áF á á á1 #3 á á á á3 á á á á á1 á75 á á áF á á á0 #4 á á á á4 á á á á 15 á56 á á áF á á á1 #5 á á á á5 á á á á á2 á58 á á áF á á á0 #6 á á á á6 á á á á á4 á80 á á áM á á á1 A.K.á - Original Message - From: Kripa R kripa...@hotmail.com To: r-help@r-project.org r-help@r-project.org Cc: Sent: Monday, August 12, 2013 6:59 PM Subject: [R] pulling out pairs from data frame Hello everyone, I'm having trouble pulling out paired samples from a data set... I have the following: reps-c(4,15) #the variable reps is a list of all paired samples data á á SameName á á á Individual á á á Age á á á Gender á á á 1 á á á 4 á á á 80 á á á M á á á 2 á á á 15 á á á 56 á á á F á á á 3 á á á 1 á á á 75 á á á F á á á 4 á á á 15 á á á 56 á á á F á á á 5 á á á 2 á á á 58 á á á F á á á 6 á á á 4 á á á 80 á á á M á I'd like to make a new variable with only the samples that have pairs. Any suggestions would be greatly appreciated Thanks! .kripa ááá ááá ááá á ááá ááá á ááá [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] pulling out pairs from data frame
I manipulated the code you sent and it works perfectly, thanks! .kripa Date: Tue, 13 Aug 2013 08:10:53 -0700 From: smartpink...@yahoo.com Subject: Re: [R] pulling out pairs from data frame To: kripa...@hotmail.com CC: r-help@r-project.org Hi, The conditions are still not clear. dat2- dat1[dat1$Individual%in% reps,] dat2 # SameName Individual Age Gender #11 4 80 M #22 15 56 F #44 15 56 F #66 4 80 M A.K. From: Kripa R kripa...@hotmail.com To: arun smartpink...@yahoo.com Cc: R help r-help@r-project.org Sent: Tuesday, August 13, 2013 10:56 AM Subject: RE: [R] pulling out pairs from data frame Oops! Ok So I have this file: SampleName Individual Age Gender 1 4 80 M 2 15 56 F 3 1 75 F 4 15 56 F 5 2 58 F 6 4 80 M And I want to pull out paired samples, so the resulting file would look something like this: SampleName Individual Age Gender 1 4 80 M 2 15 56 F 4 15 56 F 6 4 80 M .kripa Date: Mon, 12 Aug 2013 18:36:08 -0700 From: smartpink...@yahoo.com Subject: Re: [R] pulling out pairs from data frame To: kripa...@hotmail.com CC: r-help@r-project.org Hi, The question is not clear so not sure this is what you wanted. dat1- read.table(text= SameName áIndividual áAge Gender 1 4 á80 áM á 2 15 á56 F 3 1 75 áF 4 15 á56 áF 5 á2 á58 áF 6 4 á80 áM ,sep=,header=TRUE,stringsAsFactors=FALSE) reps-c(4,15)á ádat1$Newcol-as.numeric(dat1$Individual%in% reps) ádat1 # áSameName Individual Age Gender Newcol #1 á á á á1 á á á á á4 á80 á á áM á á á1 #2 á á á á2 á á á á 15 á56 á á áF á á á1 #3 á á á á3 á á á á á1 á75 á á áF á á á0 #4 á á á á4 á á á á 15 á56 á á áF á á á1 #5 á á á á5 á á á á á2 á58 á á áF á á á0 #6 á á á á6 á á á á á4 á80 á á áM á á á1 A.K.á - Original Message - From: Kripa R kripa...@hotmail.com To: r-help@r-project.org r-help@r-project.org Cc: Sent: Monday, August 12, 2013 6:59 PM Subject: [R] pulling out pairs from data frame Hello everyone, I'm having trouble pulling out paired samples from a data set... I have the following: reps-c(4,15) #the variable reps is a list of all paired samples data á á SameName á á á Individual á á á Age á á á Gender á á á 1 á á á 4 á á á 80 á á á M á á á 2 á á á 15 á á á 56 á á á F á á á 3 á á á 1 á á á 75 á á á F á á á 4 á á á 15 á á á 56 á á á F á á á 5 á á á 2 á á á 58 á á á F á á á 6 á á á 4 á á á 80 á á á M á I'd like to make a new variable with only the samples that have pairs. Any suggestions would be greatly appreciated Thanks! .kripa ááá ááá ááá á ááá ááá á ááá [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] pulling out pairs from data frame
Hello everyone, I'm having trouble pulling out paired samples from a data set... I have the following: reps-c(4,15) #the variable reps is a list of all paired samples data SameName Individual Age Gender 1 4 80 M 2 15 56 F 3 1 75 F 4 15 56 F 5 2 58 F 6 4 80 M I'd like to make a new variable with only the samples that have pairs. Any suggestions would be greatly appreciated Thanks! .kripa [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] order function
Hi I'm having a simple issue with the order function. When I use the following code my data is not ordered correctly output[order(output[,3]),] Namebeta pval 881 9.09303277751237 0.000100253350483199 74026.40553461638365 0.00010228641631914 4879 -8.88509881106217 0.000103251645995887 However when I export the data and sort it in excel I see the following: Name beta pval pval 25037 -5.70737 2.48E-07 34294 -19.6931 1.04E-05 36002 -12.2478 1.63E-05 Any suggestions on how I can get this sort to work properly on data in scientifict format? .kripa [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] order function
Hi I'm having a simple issue with the order function. When I use the following code my data is not ordered correctly output[order(output[,3]),] Namebeta pval 881 9.09303277751237 0.000100253350483199 74026.40553461638365 0.00010228641631914 4879 -8.88509881106217 0.000103251645995887 However when I export the data and sort it in excel I see the following: Name beta pval pval 25037 -5.70737 2.48E-07 34294 -19.6931 1.04E-05 36002 -12.2478 1.63E-05 Any suggestions on how I can get this sort to work properly on data in scientifict format? .kripa [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
