I have another question for you that I cannot solve myself.
I loaded my profiles and am doing ANOVA analysis.
I hybridized different timepoints, performed dye-swaps and the set-up of the
experiment is like this:
Cy5, Cy3, And dye-swap for each comparison
t0 -, t0
t0 -, t1
t0 -, t4
t0 -, t6
t0 -, t14
So, I have 10 hybridizations
I did an ANOVA with the both hybs t0 - t0 in group 1
, , , the both hybs t0 - t1 in group 2
, , , the both hybs t0 - t4 in group 3
, , , the both hybs t0 - t6 in group 4
, , , the both hybs t0 - t14 in group 5
This gave a group of genes with a p value smaller than 0.001
But I also see that some of these genes have a differential ratio for the
first group t0 - t0, but should be 0 (log-scale), as exact the same targets
Can I say somewhere that I want that as a restriction? To use only those
genes that have a small error in the t0 - t0 comparison (and its dye-swap).
I hope my question is clear to you, you can always ask if something is not
Thanks in advance!
I discussed this with a colleague in Seattle and the only way that we could
think of would be to create a bioset of the sequences in the t0 - t0
profiles and then use that bioset in a query of the ANOVA.
For example, to create the bioset you might open a combined plot for the two
t0 profiles, select all signature sequences (sequences that are
significantly different between the two profiles expected to be the same).
Next, select 'Sequence Set' from the 'Sequences' menu, give the set a name
and save it.
In your ANOVA, you can then choose 'Find and Select' from the 'Edit' menu.
Make an advanced query for "In sequence set / not equal to / sequence set
I suppose you could also do the "reverse" - make a bioset of all sequences
with log(ratio) close to zero and then do a search in the ANOVa for "In
sequence set / equal to / sequence set name".
I hope this all makes sense. Let me know if you need further clarification.