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.
You need to provide more information in your question because it's currently unanswerable.
I have performed microarray differential expression analysis using the following commands:
celFiles <- list.celfiles()
affyRaw <- read.celfiles(celFiles)
eset <- oligo::rma(affyRaw)
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:
annotLookup <- select(hgu133a.db, keys = probes,
columns = c('PROBEID', 'ENSEMBL', 'SYMBOL'))
to determine gene symbols.
Where is this probe list from? From a file, website?
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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