[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

[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] 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

[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

Re: [R] pulling out pairs from data frame

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Re: [R] pulling out pairs from data frame

. 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

[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

[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

[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