I'd like to analyze GSE18789 from GEO study mRNA expression profiling in adult mouse liver following benzo(a)pyrene (BaP) treatment [Agilent gene expression array]. I need a gene-expression matrix file in for example .CSV format and a separate matrix containing the clinical annotations of the study's samples (samples should be in rows).
How would you do this?
http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-18789/files/ to access/download file(s). The descriptions of the zipped data files are present in the respective .txt files.
You can pre-clean the already tabulated data for instance using Excel, and keep it in the original .CSV, for downstream R analyses.
Hope this answers your question.
Dear Alain
I here attach a file of how to analyze microarray data set files that u down load from Gene expression omni server of ncbi, i hope it will help you..
If u find any issues wd it please let me know i shall try to rectify to my best knowledge.
Dear @Marcin and @Goutham, many thanks for your answers. I used iPython with Pandas library to parse the data. I wrote a "recipe" in case any one needs to use it. the RPY package makes it very easy to transform the data to an R object for further R downstream analysis. I wanted to load the data in our website to then send it to GenePattern and GenomeSpace.
Here a guide for Agilent: http://community.insilicodb.com/t/how-to-convert-agilent-gene-expression-data-into-a-gene-expression-matrix/63
and one for Illumina: http://community.insilicodb.com/t/how-to-convert-illumina-gene-expression-data-into-a-gene-expression-matrix/66
Awesome!
I was JUST looking for a tool like that, for my envisioned meta-analyses. Care to get in touch with this regard some more?
We recently updated our upload tool. Hopefully muuuuch easier to use. Would love your feedback!
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