group spectral counts in Abacus

[maryamafkarian]

Hi,

 

I recently used Abacus to get spectral counts for 30 case and 30 control samples. I did this by getting counts in individual samples (60) as well as getting spectral counts for the cases and controls as groups (group 0 and group 1). Considering that for each protein, no spectra exist in a subset of samples, how does Abacus calculate the group average counts?

 

thank you,

Maryam

[Damian]

Hi
I'm not sure I understand what you did.
You had 60 pepXML and corresponding protXML files and presumably the combined protXML file.
Normally you run Abacus on all of this data combined.

>From your description, you ran Abacus on each individual experiment (all 60 XML file pairs) then averaged the results together?

Damian


maryamafkarian wrote:

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[maryamafkarian]

For the group-wise comparison, we combined the 30 files into a single pep.xml and prot.xml and also generated the combined prot.xml.  So we had one pep.xml for the entire case group and one for the entire control group (2 pep.xml files and 2 prot.xml ones and a combined prot.xml file)

[Damian]

Okay, so you are working with 5 XML files total.

In answer to your original question, Abacus does not compute group average counts.
Given that your groups do not have subsets as you describe,  the counts given by Abacus are based solely upon the peptides assigned to it. So if a protein group has 5 unique peptides with 2 spectra assigned to each one, then the spectral count total is 10 for that group.

If you want to know the spread of the spectral counts across each of the 30 cases and 30 controls you'll need to run Abacus on the all 120 pepXML and protXML files plus the combined prot.xml file.

Damian


maryamafkarian wrote:

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[maryamafkarian]

thank you.

On Thursday, March 27, 2014 10:03:43 PM UTC-7, maryamafkarian wrote: