Hi everyone:
I am running aroma.affymetrix on human exon array (HuEx-1_0-st-v2). I find
a confusing thing about the gene summary:
trFit is identical to ExFit.
My understanding is that if mergeGroups=TRUE, I may get a single value for
each transcript. for every sample,
if mergeGroups=FALSE, I will get the exon value for each transcription for
every sample, and I won't get a single value for the whole transcipt
plmTr <- ExonRmaPlm(csN, mergeGroups=TRUE)
fit(plmTr, verbose=verbose) # this takes a while!
cesTr <- getChipEffectSet(plmTr)
trFit <- extractDataFrame(cesTr, units=NULL, addNames=TRUE
plmEx <- ExonRmaPlm(csN, mergeGroups=FALSE)
fit(plmEx, verbose=verbose) # this takes a while!
cesEx <- getChipEffectSet(plmEx)
ExFit <- extractDataFrame(cesEx, units=NULL, addNames=TRUE) # this takes a
while!
Here is the part of the output:
> head(ExFit)
unitName groupName unit group cell 1 10 11 12
1 2315101 1 1 1 19.91533 28.34446 20.14796 10.92667
2 2315102 2 1 2 55.66761 77.97919 101.01392 44.96733
3 2315103 3 1 3 44.79701 73.08073 75.10196 62.49785
4 2315104 4 1 4 28.98740 24.75316 40.05618 17.43745
5 2315105 5 1 5 21.10917 23.98594 21.76450 16.75796
6 2315107 6 1 6 122.09443 105.53691 120.02885 95.87488
13 14 15 16 17 18 19
1 21.31603 29.27402 24.12943 31.18515 18.60429 24.37861 16.73564
2 39.38017 86.09061 40.92926 83.51102 76.95478 85.15944 70.13566
3 101.16308 114.98180 98.44022 119.96152 102.34689 76.80968 108.02284
4 28.26450 40.84023 29.50496 27.05476 22.28358 27.41571 17.88600
5 16.32026 14.93433 17.78723 13.53734 16.34178 13.88542 24.92704
6 132.69742 108.07824 57.43384 113.88557 91.63612 119.54205 77.06416
2 20 21 22 23 24
3 4
1 32.60419 21.11517 14.57714 27.00686 14.11651 16.30104 13.79101
19.32702
2 73.30531 75.04469 97.94950 64.71037 41.10474 42.96914 47.51828
73.33295
3 82.89948 90.72786 122.13290 59.63858 67.19086 56.18360 60.66575
121.92789
4 29.02717 43.30773 28.33748 32.22499 17.87397 23.79599 33.65727
22.60753
5 19.58357 24.72680 36.65230 8.19673 13.90474 14.41629 21.83969
12.80630
6 287.75107 184.23683 96.85452 102.10287 97.40369 76.74464 124.80372
84.51424
5 6 7 8 9
1 18.66613 17.66701 25.22667 14.51385 18.81077
2 45.13001 71.78680 59.35398 67.97990 60.44554
3 77.11916 87.39983 88.27144 75.76764 67.04836
4 24.17267 20.52709 24.53519 19.87156 11.15668
5 10.12059 19.18672 10.15962 23.18453 16.01071
6 142.90196 98.91206 117.82574 113.87852 69.68742
> head(trFit)
unitName groupName unit group cell 1 10 11 12
1 2315101 1 1 1 19.91533 28.34446 20.14796 10.92667
2 2315102 2 1 2 55.66761 77.97919 101.01392 44.96733
3 2315103 3 1 3 44.79701 73.08073 75.10196 62.49785
4 2315104 4 1 4 28.98740 24.75316 40.05618 17.43745
5 2315105 5 1 5 21.10917 23.98594 21.76450 16.75796
6 2315107 6 1 6 122.09443 105.53691 120.02885 95.87488
13 14 15 16 17 18 19
1 21.31603 29.27402 24.12943 31.18515 18.60429 24.37861 16.73564
2 39.38017 86.09061 40.92926 83.51102 76.95478 85.15944 70.13566
3 101.16308 114.98180 98.44022 119.96152 102.34689 76.80968 108.02284
4 28.26450 40.84023 29.50496 27.05476 22.28358 27.41571 17.88600
5 16.32026 14.93433 17.78723 13.53734 16.34178 13.88542 24.92704
6 132.69742 108.07824 57.43384 113.88557 91.63612 119.54205 77.06416
2 20 21 22 23 24
3 4
1 32.60419 21.11517 14.57714 27.00686 14.11651 16.30104 13.79101
19.32702
2 73.30531 75.04469 97.94950 64.71037 41.10474 42.96914 47.51828
73.33295
3 82.89948 90.72786 122.13290 59.63858 67.19086 56.18360 60.66575
121.92789
4 29.02717 43.30773 28.33748 32.22499 17.87397 23.79599 33.65727
22.60753
5 19.58357 24.72680 36.65230 8.19673 13.90474 14.41629 21.83969
12.80630
6 287.75107 184.23683 96.85452 102.10287 97.40369 76.74464 124.80372
84.51424
5 6 7 8 9
1 18.66613 17.66701 25.22667 14.51385 18.81077
2 45.13001 71.78680 59.35398 67.97990 60.44554
3 77.11916 87.39983 88.27144 75.76764 67.04836
4 24.17267 20.52709 24.53519 19.87156 11.15668
5 10.12059 19.18672 10.15962 23.18453 16.01071
6 142.90196 98.91206 117.82574 113.87852 69.68742
Thanks in advance!
--
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