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Hello folks!! Can you please suggest me, how to extract the expression data of a certain condition from a microarray data with annotation?? any suggestions will be highly appreciated!!
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The GEO page for that experiment has a link to the array used, and that page has the information provided to GEO from the people who created the array (it's a spotted array). The entirety of the data that they provide is essentially 'Unknown', and doesn't appear to include any sequences. At this point your only recourse appears to be contacting the submitter and asking them if they have any other information.
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Could you elaborate a bit more your question ? What kind of data do you have (platform, how you imported it) and do you have any relevant code to share ?
for example, if I want to extract the expression data of GSM214904 from the GEO accession number GSE8664, I used this below cod to get the expression data, now how do I annotate this data, with particular locus tag ?
library(GEOquery) library(limma) library(umap) library(affy)
load series and platform data from GEO
gset <- getGEO("GSE8664", GSEMatrix =TRUE, getGPL=FALSE) if (length(gset) > 1) idx <- grep("GPL2787", attr(gset, "names")) else idx <- 1 gset <- gset[[idx]]
gsms <- "XXX000000XXXXXX" sml <- strsplit(gsms, split="")[[1]]
samples selection within a series
sel <- which(sml != "X") # eliminate samples marked as "X sml <- sml[sel] gset <- gset[ ,sel]
ex <- exprs(gset)