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wang peter
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@wang-peter-4647
Last seen 10.3 years ago
this is output of limma
## ID logFC
AveExpr t P.Value adj.P.Val
B
## 9491 39400_at -0.9997850
5.634004
-5.727329 1.482860e-05 0.1034544 2.4458354
> eset["39400_at",]
CLL11 CLL12 CLL14 CLL15 CLL16 CLL17 CLL18
CLL19
CLL20 CLL21
5.146120 6.494292 4.912334 4.927824 5.665698 6.190625 6.843152
5.408045
6.556617 5.148195
CLL22 CLL23 CLL24 CLL2 CLL3 CLL4 CLL5
CLL6
CLL7 CLL8
6.102306 4.776241 5.534030 6.538251 5.333660 5.364452 5.815452
5.422736
4.671384 5.698590
CLL9
5.764070
we can see :AveExpr =sum(eset["39400_at",])/21;
but when i calculate the logFC, it is not -0.9997850
SampleID Disease
2 CLL11 progres.
3 CLL12 stable
5 CLL14 progres.
6 CLL15 progres.
7 CLL16 progres.
8 CLL17 stable
9 CLL18 stable
10 CLL19 progres.
12 CLL20 stable
13 CLL21 progres.
14 CLL22 stable
15 CLL23 progres.
16 CLL24 stable
17 CLL2 stable
18 CLL3 progres.
19 CLL4 progres.
20 CLL5 progres.
21 CLL6 progres.
22 CLL7 progres.
23 CLL8 progres.
24 CLL9 stable
that is the process:
sum_stable=eset["39400_at",][2]+eset["39400_at",][6]+eset["39400_at",]
[7]+eset["39400_at",][9]+eset["39400_at",][11]+eset["39400_at",][13]+e
set["39400_at",][14]+eset["39400_at",][21]>
sum=sum(eset["39400_at",])
> sum=sum(eset["39400_at",])
> sum_prog=sum-sum_stable
> ave_prog=sum_prog/13
> ave_stable=sum_stable/8
> fc=ave_prog/ave_stable
log2(fc)
-0.2513515
--
shan gao
Room 231(Dr.Fei lab)
Boyce Thompson Institute for Plant Research
Cornell University
Tower Road, Ithaca, NY 14853-1801
Office phone: 1-607-254-1267(day)
Official email:sg839@cornell.edu
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