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Old 03-19-2014, 08:00 AM   #40
shriram
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Location: UK

Join Date: May 2010
Posts: 13
Default Fold change ploting

Thank you for your reply, now I understand why there are differences at node level data and actual fold changes.
However when I want to compare the fold change that I see in the input data and on the KEGG pathway it doesn't correlate well.
e.g.
pv.out.list[[1]]
Gene A:
T1 T2 T3 T4 T5
0.66 4.1079 0.830 3.278 2.71

input fold change values:
Gene A
-1.2 0.7 -0.14 -0.48 -0.78

Color coding for this gene on pathway node:

#EF3030 #FF0000 #FF0000 #FF0000 #FF0000

which doesn't reflect the trend seen in the input data.

When I change node.sum="median" it little bit shows same trend as input fold changes.
pv.out.list[[1]]
-1.15 0.7626 0.000 1.387 1.534
#00FF00 #EF3030 #BEBEBE #FF0000 #FF0000

It is bit confusing for me.


Thanks
shriram is offline   Reply With Quote