Hi all,
I noticed recently that for all my recent analyses that there is not external scaling of abundances when comparing between conditions (external scaling factor is set to 1.0 for all samples in read_groups.info file).
This is in contrast to the internal scaling factor which is almost always different from 1, indicating that abundances between conditions are being adjusted for various factors.
My question is whether or not this is common or a result of a particular parameter that is being set by default by cuffdiff. I am simply using the UCSC gtf file as my reference annotation. Thanks again for all of your help, this forum has been great.
I noticed recently that for all my recent analyses that there is not external scaling of abundances when comparing between conditions (external scaling factor is set to 1.0 for all samples in read_groups.info file).
This is in contrast to the internal scaling factor which is almost always different from 1, indicating that abundances between conditions are being adjusted for various factors.
My question is whether or not this is common or a result of a particular parameter that is being set by default by cuffdiff. I am simply using the UCSC gtf file as my reference annotation. Thanks again for all of your help, this forum has been great.
