Cuffnorm Normalization: Per condition or across all samples ?

[vramnarine]

Hi All

I am using the new workflow of:

Cufflinks -> Cuffmerge -> Cuffquant -> Cuffnorm

When supplying a sample sheet (using parameter: --use-sample-sheet) , I must designate conditions per sample.

My question is, does cuffnorm normalize for library depths within a condition ? or across all of your samples ? If it is per condition, is there a way to set cuffnorm to normalize across all samples?

When I change the condition label (column in my sample sheet) of my samples to all the same condition (so that normalization will occur across all samples), cuffnorm fails saying it needs at least 2 samples to run (when there actually is more than 2 samples just all with the same condition), so I am forced to add condition labels to my samples AND most importantly making me think the normalization occurs per condition and not across all your samples.

Any clarity would be much appreciated!