I want to integrate expression values into my network. For this purpose, I selected Dataset GSE29801 (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE29801). After assigning samples to each group, adjustment to the P-values was applied with the Benjamini & Hochberg false discovery rate method which is selected by default in GEO2R options. After calculation, I saved all results. But, the complete results table was not complete!!
There was 20330 IDs in this table, whereas 41000 IDs were existed in series matrix file of GSE29801. Almost half of genes were not included in the result table. Therefore, I would not able to enrich all the nodes in my network with their related P-values.
I don't know what the problem is. I would appreciate any suggestion.