Why there are same name with different value in my microarray result?

Question

[Aki]

I have done one color agilent microarray. I am processing my data, but my data showed one miRNA present in more than one place with different value. Could someone please tell me what is the reason for this? Thanks!

probeset.list <- topTable(CaseControl.fitmodel.eBayes, number=99999, adjust.method="BH", sort.by="P", lfc=1)
probeset.list
      Row Col ControlType      ProbeName     SystematicName     logFC
57521 378  16           0     A_54_P3055     mmu-miR-18b-5p -1.336475
56668 372  89           0 A_54_P00005073     mmu-miR-668-5p -1.304100
11303  74 140           0     A_54_P2311     mmu-miR-144-3p  1.605108
5503   36 146           0     A_54_P2158        mmu-miR-718 -1.488318
20927 137 155           0 A_54_P00006996    mmu-miR-7211-3p  1.352514
31262 205 119           0     A_54_P2312     mmu-miR-144-3p  1.911592
1731   12  33           0     A_54_P2312     mmu-miR-144-3p  1.528154
50175 329 156           0     A_54_P2312     mmu-miR-144-3p  1.358575
33518 220 106           0     A_54_P2311     mmu-miR-144-3p  1.471959

Answer 1

[JC]

It is common to add multiple replicates in miRNA microarrays, if you see the Column and Row values, the spots are in different places.

[Aki]

Thank you JC! Do you know how to combine these spots as one miRNA? Or do we treat them differently?

[JC]

You use them as technical replicates in your analysis

[Aki]

Thanks. I have solved with avereps function.