I'm trying to analyze the microarray dataset GSE38063 on GEO2R to determine which genes are deferentially expressed when comparing muscle of humans on caloric restriction (CR) or Western Diet (WD). However excel output from GEO2R presents 16163 out of the 21179 genes as deferentially expressed when utilizing adjusted p-value < 0.05.
I'm guessing this is because the microarray results are not normalized as shown on the boxplot attached, obtained from GEO2R. WD samples presents higher mean values compared to CR samples.
Is the lack of normalization the cause of this weird result? How could I normalize the data and analyze in a way that does not require a lot of programming expertise?
@ Thiago Leite Knittel
Dear Thiago,
That is a nice question. Are you still dealing with your mentioned problem or is it solved now?
Sincerely yours,
Amir
Hello Thiago Leite Knittel . In case you are having the same problem, you can try "Force normalization" in the option center of GEO2R. You can also adjust your p value from the option center. Also can try by selecting the genes with lesser p value for more specific and high significant genes.
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