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Control 5 mM LiCl 25 nM Rap 5 mM LiCl + 25 nM 30 mM LiCl IL-1B
Rap
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Control 5 mM LiCl 30 mM LiCl IL-1B
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Control 5 mM LiCl 30 mM LiCl
1. log transformation: reduce the effect of outliers, attribute equal weight to all data points

Ct Brach (GOI) Ct Actb (REF) dCt ddCt fold

Control 24.2 17.7 6.5 0.0 1.0

Activin A 3ng/ml 21.3 18.1 3.2 -3.3 9.8
Activin A 30ng/ml 26.0 17.4 8.6 2.1 0.2
Control(2) 24.7 18.9 5.8 0.0 1.0
Activin A 3ng/ml(2) 22.2 17.8 4.4 -1.4 2.6
Activin A 30ng/ml(2) 23.8 17.5 6.3 0.5 0.7
Control(3) 27.0 17.5 9.5 0.0 1.0
Activin A 3ng/ml(3) 24.5 18.1 6.4 -3.1 8.6
Activin A 30ng/ml(3) 29.6 18.7 10.9 1.4 0.4

2. mean centering: equalize the experimental averages

Ct Brach (GOI) Ct Actb (REF) dCt ddCt fold

Control 24.2 17.7 6.5 0.0 1.0

Activin A 3ng/ml 21.3 18.1 3.2 -3.3 9.8
Activin A 30ng/ml 26.0 17.4 8.6 2.1 0.2
Control(2) 24.7 18.9 5.8 0.0 1.0
Activin A 3ng/ml(2) 22.2 17.8 4.4 -1.4 2.6
Activin A 30ng/ml(2) 23.8 17.5 6.3 0.5 0.7
Control(3) 27.0 17.5 9.5 0.0 1.0
Activin A 3ng/ml(3) 24.5 18.1 6.4 -3.1 8.6
Activin A 30ng/ml(3) 29.6 18.7 10.9 1.4 0.4

3. autoscaling: equalize experimental standard deviations

+ extra step (multiplication by the mean exp. standard deviation) to make the fold changes reflecting the origi

Ct Brach (GOI) Ct Actb (REF) dCt ddCt fold

Control 36.7 26.2 10.5 0.0 1.0

5 mM LiCl 32.6 26.5 6.0 -4.5 21.9
25 nM Rap 34.2 26.7 7.5 -2.9 7.7
5 mM LiCl + 25 nM Rap 32.4 27.0 5.4 -5.0 32.9
30 mM LiCl 30.7 26.9 3.9 -6.6 97.0
IL-1B 28.3 26.3 2.0 -8.5 355.2
Control (2) 35.3 25.2 10.0 0.0 1.0
5 mM LiCl 32.7 25.9 6.8 -3.3 9.6
25 nM Rap 34.4 26.3 8.2 -1.9 3.7
5 mM LiCl + 25 nM Rap 32.2 26.2 6.1 -4.0 15.6
30 mM LiCl 28.8 25.9 2.9 -7.2 144.0
IL-1B 26.2 25.1 1.1 -8.9 476.0
Control(3) 36.5 24.9 11.6 0.0 1.0
5 mM LiCl 34.1 25.1 8.9 -2.6 6.2
25 nM Rap 36.0 25.3 10.7 -0.8 1.8
5 mM LiCl + 25 nM Rap 34.1 25.7 8.5 -3.1 8.7
30 mM LiCl 31.8 25.9 5.8 -5.8 53.9
IL-1B 30.6 26.3 4.3 -7.3 160.0
 log (fold) Avg SEM lower95%CI

0.0000 Control 0.0000 0.0000 0.0000

0.9934 Activin A 3ng/ml 0.7827 0.1815 0.0020
-0.6322 Activin A 30ng/ml -0.4014 0.1394 -1.0012
0.0000
0.4214
-0.1505
0.0000
0.9332
-0.4214

log (fold) exp. average mean centered Avg

0.0000 0.1204 -0.1204 Control -0.1271

0.9934 0.8730 Activin A 3ng/ml 0.6556
-0.6322 -0.7526 Activin A 30ng/ml -0.5285
0.0000 0.0903 -0.0903
0.4214 0.3311
-0.1505 -0.2408
0.0000 0.1706 -0.1706
0.9332 0.7626
-0.4214 -0.5920

nges reflecting the original experimental fold changes

log (fold) exp. average mean centered exp. stDev

0.0000 1.3805 -1.3805 0.8838

1.3408 -0.0396
0.8879 -0.4926
1.5168 0.1363
1.9869 0.6065
2.5505 1.1700
0.0000 1.2625 -1.2625 0.9970
0.9810 -0.2815
0.5645 -0.6980
1.1938 -0.0688
2.1583 0.8958
2.6776 1.4150
0.0000 0.9864 -0.9864 0.8474
0.7914 -0.1950
0.2529 -0.7334
0.9377 -0.0487
1.7319 0.7456
2.2042 1.2179
upper95%CI linAvg LinLCI LinUCI

0.0000 1.0000 1.0000 1.0000

1.5634 6.0629 1.0045 36.5935
0.1984 0.3969 0.0997 1.5791

SEM lower95%CI upper95%CI linAvg LinLCI

0.0234 -0.2278 -0.0264 0.7463 0.5918

0.1653 -0.0557 1.3669 4.5246 0.8795
0.1511 -1.1786 0.1217 0.2962 0.0663

autoscaled autoscaled Avg SEM lower95%CI upper95%CI

multiplied by
mean exp. stDev

-1.5620 -1.4205 -1.2102 0.1085 -1.6771 -0.7433

-0.0449 -0.0408 -0.1689 0.0655 -0.4509 0.1130
-0.5574 -0.5069 -0.6435 0.0810 -0.9919 -0.2952
0.1542 0.1402 0.0084 0.0660 -0.2755 0.2923
0.6862 0.6240 0.7471 0.0617 0.4815 1.0127
1.3239 1.2039 1.2672 0.0320 1.1296 1.4048
-1.2663 -1.1516
-0.2824 -0.2568
-0.7001 -0.6367
-0.0690 -0.0627
0.8985 0.8171
1.4193 1.2907
-1.1640 -1.0585
-0.2301 -0.2092
-0.8655 -0.7871
-0.0575 -0.0523
0.8799 0.8001
1.4372 1.3070
recalAvg recalLCI RecalUCI LoBar UpBar

1.0000 1.0000 1.0000 0.0000 0.0000

6.0629 1.0045 36.5935 5.0584 30.5306
0.3969 0.0997 1.5791 0.2971 1.1823

LinUCI recalAvg recalLCI RecalUCI

0.9411 1.0000 0.7930 1.2611

23.2754 6.0629 1.1786 31.1888
1.3234 0.3969 0.0888 1.7733

linAvg LinLCI LinUCI recalAvg

0.0616 0.0210 0.1806 Control 1.0000

0.6777 0.3541 1.2972 5 mM LiCl 10.9967
0.2272 0.1019 0.5068 25 nM Rap 3.6869
1.0195 0.5303 1.9601 5 mM LiCl + 2 16.5428
5.5858 3.0305 10.2956 30 mM LiCl 90.6327
18.5008 13.4763 25.3986 IL-1B 300.1872

Control 1.0000
5 mM LiCl 10.9967
30 mM LiCl 90.6327
IL-1B 300.1872
LoBar UpBar

0.2070 0.2611
4.8843 25.1259
0.3080 1.3765

recalLCI RecalUCI LoBar UpBar

0.3412 2.9305 0.6588 1.9305

5.7454 21.0476 5.2513 10.0509
1.6531 8.2228 2.0338 4.5359
8.6048 31.8036 7.9380 15.2608
49.1718 167.0528 41.4609 76.4202
218.6622 412.1078 81.5251 111.9205

0.6588 1.9305
5.2513 10.0509
41.4609 76.4202
81.5251 111.9205