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]+eset["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
Facebook:http://www.facebook.com/profile.php?id=100001986532253

	[[alternative HTML version deleted]]

