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J-Express => Forum => Topic started by: MariB on April 12, 2012, 10:31:53 AM



Title: Fold change between groups
Post by: MariB on April 12, 2012, 10:31:53 AM
I am comparing fold change between groups. This should be the ratio between the averages of the two groups I am comparing. However the average and resulting fold change values  (values both given as outputs in Jexpress) are different from the averages I calculate myself. My data are log-transformed. How does Jexpress calculate averages and fold change?

-Mari Bratberg:)


Title: Re: Fold change between groups
Post by: annekristin on April 12, 2012, 03:13:43 PM
I just checked this and see a problem. I will look into it a bit more, but there may be a bug in the way the Fold Change Viewer is calculating the fold change.

In the mean time you can use e.g. SAM to calculate the fold change. SAM calculates fold change this way:

2^( mean(groupA) - mean(groupB) )


Title: Re: Fold change between groups
Post by: RBE on April 13, 2012, 02:00:09 PM
I have a kind of related question. After running SAM I would like to filter my results using SAM selection. For example I would like to set the FDR to be between 0 and 0.05 and fold change to be at least 1.5.  When setting the FDR I get more selected when using 0 to 0.01 than 0 to 0.05, and using the Fold change filter doesn't seem to work at all.
Unable to make selection. See reason below. java.lang.numberformatexception: For input string:"-1,206.533"   ???
Rolf


Title: Re: Fold change between groups
Post by: HCJ on September 12, 2012, 08:46:04 PM
I just checked this and see a problem. I will look into it a bit more, but there may be a bug in the way the Fold Change Viewer is calculating the fold change.

In the mean time you can use e.g. SAM to calculate the fold change. SAM calculates fold change this way:

2^( mean(groupA) - mean(groupB) )

Any answers to this problem yet? I am confused as to this problem as well.