Question

GEO2R Gene Expression

1

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nkline ▴ 10

@nkline-15239

Last seen 6.1 years ago

Hello,

I would like to automate the following process that uses GEO2R to analyze gene expression. For each contig I provide, this is the workflow I follow:

browse to https://www.ncbi.nlm.nih.gov/geo/geo2r/?acc=GSE36545
click Profile Graph
Enter ID: assembledIsotigs_Contig9526
click Set
click Sample Values
copy results from pop-up window:

Instead of going through the above workflow for each contig, is it possible to automate the process using something like the getGEO() function ?

Thanks!

geoquery • 1.3k views

ADD COMMENT • link updated 6.1 years ago by Sean Davis 21k • written 6.1 years ago by nkline ▴ 10

score 1 · Answer 1 · 2018-03-14

1

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Sean Davis 21k

@sean-davis-490

Last seen 4 months ago

United States

How about something like this:

library(GEOquery)
g = getGEO('GSE36545')[[1]]
barplot(exprs(g)['assembledIsotigs_Contig9526', ], horiz = TRUE, las=2, cex.names = 0.5)

Tinker with the plot to order samples as you see fit. For example, to order by tumor status:

barplot(exprs(g)['assembledIsotigs_Contig9526', order(pData(g)[, 'tumor status:ch1'])], horiz = TRUE, las=2, cex.names = 0.5)

ADD COMMENT • link 6.1 years ago Sean Davis 21k

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Thanks Sean. Now I know how to create a bar plot. Ultimately, I would like the result as a tab-delimited file with sample, title, and value (just like it appears in the image above). Any idea how to make that happen with getGEO()?

ADD REPLY • link 6.1 years ago nkline ▴ 10

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tabler = function(g, gene_id) { 
    vals = exprs(g)[gene_id, ] 
    pd = pData(g) 
    return(data.frame(sample = sampleNames(g), title=pd$title, values = vals )) 
} 
tabler(g, "assembledIsotigs_Contig9526")

ADD REPLY • link 6.1 years ago Sean Davis 21k