Hi!
I'm looking at this study Article Mice Fed Rapamycin Have an Increase in Lifespan Associated w...
, and their excel microarray data has negative log2 values, which doesn't make sense to me. Can anyone explain how to read this? I am interested in the data for SDH subcomplexes SDHD, SDHC, and SDHB. Thanks so much in advance.
Log2 transformed values < 0 arise from untransformed values < 1. What kind of values are log2 transformed? If it is fold changes than negative values indicate downregulation as Tommaso already mentioned. If they are just expression measures than the untransformed values are small (< 1). Another option could be that the negative values arose due to some kind of background subtraction.
Comparing the expression profiles of A vs B, usually, negative values refer to genes which are upregulated in B, whereas positive values are about genes that are upregulated in A
Log2 transformed values < 0 arise from untransformed values < 1. What kind of values are log2 transformed? If it is fold changes than negative values indicate downregulation as Tommaso already mentioned. If they are just expression measures than the untransformed values are small (< 1). Another option could be that the negative values arose due to some kind of background subtraction.
I agree with Markus, except for his last sentence. Background subtraction is (should be) done on untransformed values (subtracting logs would mean to divide signal intensities, what is not a sensible background correction). If signals are subtracted, it can happen that negative corrected signals (still untransformed values) are obtained, and it is not possible to log-transform non-positive values. Such values would be missing (NA) in the log-transformed representation.
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