Dear Dr. Smyth.

Would you be that kind to help me on deciding whether yes or no to filter my microarray data set with a filtering method correcting for variance such as I/NI method from Talloen et al. (2007). Whereas many researchers say that filtering should increase the power of the test, then increasing the chance to get true deferentially expressed genes. However when I analyzed my data set. I found the next: (meaning lower number of DEG when filtering).




Ortoghonal contrasts                # of genes
 (adjustedP >0.05 and   FC >1.4)
w/o filtering   I/NI filtering
FAT        195    118
FA         329    151
MR         169    103
FAT by MR          854    321
FA by MR          961     283

Also, I found that Bourgon et al. (2010) do not recommend to combine the use of  limma t-statistic with filtering. So please, I will appreciate your suggestion on whether filter or not filter my data set.

Thanks in advance.
Miriam



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Miriam Garcia, MS, PhD
Department of Animal Sciences
University of Florida


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