Hello everybody,
first of all, thanks for providing this forum, it really helps me alot in my
data analysis. :)
second, my problem: I have 2 costum exon CDFs with CEL files respectively. I
want to find differential splicing using FIRMA. It seems that I have after
applying the commands from the aroma.org vignette:
plmTr <- ExonRmaPlm(csN, mergeGroups=TRUE)
fit(plmTr, unit=NULL, verbose=verbose, force=force) # this takes a while!
firma <- FirmaModel(plmTr)
#print(str(firma))
fit(firma, verbose=verbose) # this takes a while!
# get the firma scores
fs <- getFirmaScores(firma)
#print(str(fs))
# take the log2 of the firma scores
fsScores <- log2(extractDataFrame(fs))
no group information is available, I have only annotations based on exons:
> str(fsScores)
'data.frame': 143259 obs. of 9 variables:
$ unit : num 0 1 1.58 2 2.32 ...
$ group : num 0 0 0 0 0 0 0 0 0 0 ...
$ cell : num 0 1 1.58 2 2.32 ...
$ caquinof_20090625_Flower1_Affy_new-v4: num 0.235 -0.183 -0.177 -0.111
-0.094 ...
$ caquinof_20090625_Flower2_Affy_new-v4: num 0.02462 -0.21418 -0.00289
-0.04531 0.03572 ...
$ caquinof_20090625_Flower3_Affy_new-v4: num -0.0528 -0.2674 0.0483
-0.0398 -0.0789 ...
$ caquinof_20090625_Leaf1_Affy_new-v4 : num -0.0151 -0.1455 -0.3472
-0.2368 -0.0481 ...
$ caquinof_20090625_Leaf2_Affy_new-v4 : num -0.207 -0.0648 -0.1754
-0.1012 -0.4942 ...
$ caquinof_20090625_Leaf3_Affy_new-v4 : num -0.194 0.1359 0.1802 -0.4697
0.0343 ...
were variables 4-6 are flower replicates and 7-9 leaf replicates of
arabidopsis plant.
But I can get the group information (exons per transcript) from the exon
annotation:
one example:
exon annotation = 'AT1G01040.0.Chr1.plus.26862.27012'
transcript annotation = 'AT1G01040.0'
Now, I want to 'insert' the transcript annotation as 'group' variable and I
found the method 'SetMergeGroup':
I tried to use it like this:
setMergeGroups(groupSet[,2])
but then comes the Error
Fehler in UseMethod("setMergeGroups") :
nicht anwendbare Methode für 'setMergeGroups' auf Objekt der Klasse
"c('double', 'numeric')" angewendet
which means this:
Error in UseMethod("setMergeGroups"):
not applicable method for 'setMergeGroups' for object of the class
"c('double',
'numeric')" applied.
Could you tell me how to use tis method properly? Do I have some wrong
assumptions in my data processing step?
thanks alot for your expertise in advance,
Best wishes,
Marlen Müller
Masterstudent at the Plant Biotechnology Group,
ETH Zurich
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