As you might know that some of the datasets in GEO will contain the data in SOFT formatted files instead of CEL files which contains the abundance of the transcripts.
Do we need to consider these values as the absolute expression values and do further analysis like Differentially Expressed Genes or are there any other way/tool/algorithm s that will handle SOFT files?
The soft files and matrix files from GEO contain metadata and abundance data about the experiment. The data has already been normalised and so can be analysed directly for differentially expressed genes etc. The files can be openned in excel and then imported into other analysis software e.g. bioconductor, Genespring etc. The information on how the data has been normalised should be in the GEO record.
The soft files and matrix files from GEO contain metadata and abundance data about the experiment. The data has already been normalised and so can be analysed directly for differentially expressed genes etc. The files can be openned in excel and then imported into other analysis software e.g. bioconductor, Genespring etc. The information on how the data has been normalised should be in the GEO record.
Hi Neil,
Thanks for the reply. I will try to search and implement the bioconductor packages to analyse the SOFT files. But are these soft files created by GEO based on their algorithm or submitted by the supplier. Which is the usual case??
The soft files are always generated by GEO, based on the information provided by the submitter of the data.
To load the soft files have a look at:
http://www2.warwick.ac.uk/fac/sci/moac/people/students/peter_cock/r/geo/
Hi Neil,
The link is useful for exporting GDS files and i have GSE soft files (TimeCourse). The GeneSpring tool is a commerical one from Agilent. Do you know by any chance some free tools which can be useful for analyzing SOFT format files.
Hi
If you download all the soft files and data text files, you should be able to open them in excel. You can delete the information you do not need, leaving just the expression data. You should be able to load this into R/Bioconductor and analyse it.
Hi,
I downloaded te soft data and loaded directly on R using the comands on Neil Graham link:
#Or, open an existing GDS file (even if its compressed):
gds858
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