How to extract the numerical expression values for plotting time series curves for this Custom Yeast Genomic 70-mer Oligonucleotide Microarray NCBI GEO dataset?
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5.2 years ago
tfhahn ▴ 50

How to extract the numerical expression values for plotting time series curves for this Custom Yeast Genomic 70-mer Oligonucleotide Microarray NCBI GEO dataset?

I would like to plot the mRNA expression time series curves based on the data of the following NcBI GEO dataset.

Series GSE3705

The title of this dataset is:

JM43 cells grown aerobically in galactose and treated with Antimycin A

The URL of this dataset is:

https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE3705

The citation of the publication, which goes along with this dataset, is:

Lai LC, Kissinger MT, Burke PV, Kwast KE. Comparison of the transcriptomic "stress response" evoked by antimycin A and oxygen deprivation in Saccharomyces cerevisiae. BMC Genomics 2008 Dec 23;9:627. PMID: 19105839.

This publication is free available at https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2637875/

My problem is that the platform is

GPL1535 Custom Yeast Genomic 70-mer Oligonucleotide Microarray

What do I need to do to extract the numerical gene expression values from this dataset, which are most meaningful for plotting time series curves?

Thanks a lot

Thomas

R time series annotation transcription • 1.5k views
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Entering edit mode
5.2 years ago

The GEOquery package from bioconductor will take the GSE and pull the normalised data into R for you. You can then use libraries such as ggplot2 to perform plotting, and add features such as regression curves. You can download the respective annotation for the custom array from here

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5.2 years ago
tfhahn ▴ 50

Thank you! That helps a lot. This means I can use my old script because it seems that I only need to replace the annotation file and everything else should work the same way. Thanks for providing exact links pointing directly to the information I need.

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