Hi,
Okay, I did not know you should log2 transform before uploading. There is a normalization process in metaboanalyst. So that is not to be used?
I noticed that with my metabolomics data, the volcano plot stayed the same when I used my untransformed data versus the log2 transformation using the normalization tool in metaboanalyst. Then I read at the FC page, that for FC calculation the data before column wise normalization (in my case Log2 transformation) is used because the column wise normalization significantly changes the FC.
Then I started reading the internet, which mostly gives info for transcriptomics and proteomics data, that Log2FC = mean(log2(condition1)) - mean(log2(condition2)) is common. So, I wondered why this is common for these types of datasets, but metaboanalyst says the FC is altered significantly and that is why the original data is used. Why this difference?
Then I read the topic that I also commented on (Order of operation for fold change and p values - MetaboAnalyst - OmicsForum), from someone that had almost the same question as me. She put her data in metaboanalyst and there the FC calculation did not change when she log transformed in the normalization option of metaboanalyst. With express analyst, log transformation did change the FC, as she expected.
My question is: why this difference between metaboanalyst and expressanalyst? Is there a reason why in metaboanlayst it is specifically mentioned that FCs are calculated on non-columnwise normalized data, while in expressanalyst this does happen.
I hope this is clear.
Best,
Lonneke