Question: Question on fold change calculation for microarray data
0
gravatar for Claudia
2.7 years ago by
Claudia10
Sweden
Claudia10 wrote:

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.

limma logfc fold change • 574 views
ADD COMMENTlink modified 2.7 years ago by Gordon Smyth37k • written 2.7 years ago by Claudia10
Answer: Question on fold change calculation for microarray data
0
gravatar for Gordon Smyth
2.7 years ago by
Gordon Smyth37k
Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
Gordon Smyth37k wrote:

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?

ADD COMMENTlink modified 2.7 years ago • written 2.7 years ago by Gordon Smyth37k
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