Question on fold change calculation for microarray data
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Claudia ▴ 10
@claudia-6236
Last seen 6.1 years ago
Sweden

Dear list,

I'm sorry as this is probably an easy question but I would greatly appreciate some help. I'm trying to reanalyze some published microarray data. I have two conditions (fasted and sated state) and 12 samples for each condition (before and after food intake). I'm interested in what happens to expression values after food intake.

I analyzed the data with oligo and limma, obtaining results similar to the ones reported by the original paper, except for the fact that all logFCs have the opposite sign. The paper report results following food intake. Genes with a negative logFC are reported to be "mRNA transcripts that were downregulated following food intake." and viceversa.

If a gene is downregulated after food intake, I would expect expression values to be higher in subjects before food intake and lower after the meal, and this is what I obtain in my results. However, it seems to me that logFCs in the paper are calculated with the formula "fasted status - sated status" rather then "sated - fasted". 

Here is a numerical example for one gene for which limma gives me a positive logFC (because I think my difference is condition 2- condition 1), while in the paper a negative one is reported.

Before      After

2.535874 3.338275
1.848516 3.489296
2.441438 3.575736
2.267925 3.471507
4.501792 2.940529
3.782247 3.72118
2.324975 3.137744
1.522946 2.713971
2.773406 4.197833
1.225246 2.245911
2.505903 4.631013
2.531383 3.708032

Is my reasoning wrong to calculate gene expression variation after food intake?

Thanks a lot for your precious help.

logfc limma fold change • 1.1k views
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Entering edit mode
@gordon-smyth
Last seen 51 minutes ago
WEHI, Melbourne, Australia

It is perfectly correct to estimate the After - Before comparisons. It is also correct to do it the other way around. The results will be identical except that the logFCs will change sign. You just have to report correctly which way you did it when you publish or interpret your results.

From what you say, it would appear that the published paper may have reported the comparison incorrectly. Is the quote that you give taken verbatim from the published paper?

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