How to compare logratiofc to control group

Question

[anm17]

Hey people,

I am trying to recalculate the results of one series (GEO) but having trouble getting the same results , these are my steps :

1. got raw data (.cel files)
2. Normalized them using the method (Mas5)
3. Log transformation
4. Mean value of each group of samples:(f.e: gr1.mean,gr2.mean,..,control.mean)
5. Calculating the ratio(according to paper): gr1cratio= gr1.mean-control.mean -gr2cratio =gr2.mean-control.mean
6. 2^(ratio values)

Then I get (for example ) such a table :

         gr1ratio gr2.ratio
  Gene1   2           14
  Gene2   5           6
  Gene3   2           2
  Gene4   5           8

So they say in the paper they selected only the transcripts that are twofold up or down compared to control. Does it mean that when I have a 2 in the table that the fold change is 2 and therefor it twofold up? This would not match with the result they are presenting in their paper , and based on this there would not be values that are twofold down anyway

I tried to use their normalized data , they are providing for each sample separately on the GEO , but I again could not reach their results .

So what I am missing .. Do I have to compare the values of the table with log (mean value of the control group ) or maybe with the normalized(mean value of the control group) ?

Thank you very much !

Answer 1

[WouterDeCoster]

Make sure you don't mix up fold change and log(2) fold change!