how to create a character vector in R
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9 weeks ago

Hello,

Can anyone help me make a character vector in R with 16384 unique and non sequential values without having to type all of them in?

For example, probes <- c( "212375_at", "218706_s_at".......).

Thanks in advance for your help.

vector r microarray character analysis • 377 views
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You need to provide more information in your question because it's currently unanswerable.

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I have performed microarray differential expression analysis using the following commands:

library("arrayQualityMetrics")
library(GEOquery)
library(oligo)
library(Biobase)
library(affy)
library("splitstackshape")
library("tidyr")
library("dplyr")


celFiles <- list.celfiles()
affyRaw <- read.celfiles(celFiles)
eset <- oligo::rma(affyRaw)
library(limma)
pData(eset)
Groups <- c("DDLPS", "DDLPS", "WDLPS", "WDLPS")
design <- model.matrix(~factor(Groups))
colnames(design) <- c("DDLPS", "DDLPSvsWDLPS")
fit <- lmFit(eset, design)
fit <- eBayes(fit)
options (digits =2)
res <- topTable (fit, number = Inf, adjust.method = "none", coef = 1)
write.table(res, "diff_exp.txt", sep= "\t)

However, I do not know which specific genes were differentially expressed as I only have probe names in the excel file. I need to convert the probe names to gene id. In order to do this I need to make a character vector with probe names and then use following commands:

require(hgu133a.db)
annotLookup <- select(hgu133a.db, keys = probes,
  columns = c('PROBEID', 'ENSEMBL', 'SYMBOL'))

to determine gene symbols.

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Where is this probe list from? From a file, website?

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Thanks for your reply, my probe list is a txt file and a column in excel file with my p values from differential gene expression.

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