I want to draw a trend of the expression of genes which i have and for doing so i want to know whether the samples in GEO series matrix (I mean GSMxxxxxx) are comparable with each other (sth like normalization and these processes happened to them) or not? and also whats the meaning of this caution in GEO that i attached to my question?
thanks
Hi,
Basically a GSExxxx series file contains a set of GSMxxxx files, which are unique and processed similar, with same normalization, same platform etc and they are comparable among.
These are submitted by any scientific community, which may as part of their research work. Those data are available publicly for making it useful for other people with similar studies.
The caution says, the GEO database accepts data sets from a submitter and it should be annotated and proved by the users.
Not directly. The might be comparable to a certain degree after a common normalization, but even then it is important to consider the experimental differences (cell types/extraction, passage numbers, RNA isolation, amplification and labelling procedures). It is very dangerous to interpret differences between groups that are taken from different experiments/series, as there might be a serieous confounding of experimental conditions and the groups.
As Jochen mentioned, different data sets have different technical factors impacting the measurements. What I think would be reasonable is to extract raw data from GEO (.CEL files), try the same normalisation on the data sets but also investigate batch effects with clustering or PCA before you make any conclusion about trends.
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