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Your question could use some more information and explanation about the exact situation and scope of your analysis.
Thanks for your response, i am new to handling microarray data. my boss has asked me to find the genes for multiple abiotic stress using data from NCBI GEO. In the process i have came across the signal intensity values generated from MAS5.0 and GCOS having values eg: 364, 311, 259 etc., for control and treatments. out of total set of probes i want to select genes which have -/+4 fold change.For this i want to know what is the procedure to estimate/calculate the change in gene expression from raw data. please let me know any further clarification. your help mean a lot to me
You may want to have a look at this tutorial: Analysing Microarray Data In Bioconductor
You can't use the raw values for probes/genes straight out GEO. You would need to normalize data/analyze a set of samples to get relative expression measurements (up or down expression). You would either need to use local software (commercial and/or R/packages) to do that analysis. GEO also makes an interactive tool available GEO2R that may be enough for you needs. Check it out here.
It might be better for you to work with p-values or confidence intervals, rather than fold-changes, in this setting. You can readily detect 4-fold changes in a microarray experiment, but much less readily reproduce those changes.
dear all thanks for your quick response, i want find genes from multiple series eg: GSE3053 GSE4438 GSE4471 GSE5167 GSE6719 GSE6720 GSE6737 which belong to one platform GPL2025. in this regard suggest me the best way to find the common genes which were deferentially expressed on all the experiments
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