Hi all,
I am processing some affymetrix exon arrays and trying to compute FIRMA scores.
I did this for all CEL files and now I just want to exclude some CEL files from
the analysis without removing them from the rawData folder
(rawData/mice2010/MoEx-1_0-st-v1/). I use the extract method to select 38 of
the 107 files CEL files.
...
cs <- AffymetrixCelSet$byName("mice2010", cdf=cdf)
cs=extract(cs,1:38)
....
In the message I get from running the code I can see a line saying " Reading
residuals unit by unit for 107 arrays...done" and I was wondering if this means
that all 107 files were used in fitting the firma model or not.
Thanks,
Adi
.........
20110921 10:13:29| Array #37 ('102_R860')...done
20110921 10:13:29| Array #38 ('107_R955')...
20110921 10:13:29| Pathname:
plmData/mice2010,coreR1,A20080718,MR,QN,RMA,merged/MoEx-1_0-st-v1/107_R955,residuals.CEL
20110921 10:13:29| Already calculated.
20110921 10:13:29| Array #38 ('107_R955')...done
used (Mb) gc trigger (Mb) max used (Mb)
Ncells 451249 24.1 818163 43.7 818163 43.7
Vcells 1233293 9.5 2371218 18.1 2104276 16.1
20110921 10:13:34|Calculating PLM residuals...done
20110921 10:13:34|Fitting model of class FirmaModel...
FirmaModel:
Data set: mice2010
Chip type: MoEx-1_0-st-v1,coreR1,A20080718,MR
Input tags: coreR1,A20080718,MR,QN,RMA,merged
Output tags: coreR1,A20080718,MR,QN,RMA,merged,FIRMA,medres
Parameters: (probeModel: chr "pm"; shift: num 0).
Path:
firmaData/mice2010,coreR1,A20080718,MR,QN,RMA,merged,FIRMA,medres/MoEx-1_0-st-v1
RAM: 0.00MB
20110921 10:13:34| Identifying non-estimated units...
20110921 10:13:37| Identifying non-assigned units in FIRMA file...
20110921 10:13:37| Pathname:
firmaData/mice2010,coreR1,A20080718,MR,QN,RMA,merged,FIRMA,medres/MoEx-1_0-st-v1/009_R884,FIRMAscores.CEL
20110921 10:13:37| Identifying non-assigned units in FIRMA file...done
20110921 10:13:37| Reading data for these 17831 units...
20110921 10:14:24| Looking for pixels == 0 indicating non-assigned units:
int [1:17831] 1 2 3 4 5 6 7 8 9 10 ...
............
10:16:31| readCelUnits() of AffymetrixCelSet...done
20110921 10:16:31| Calling readUnits() in superclass...done
20110921 10:16:35| Reading residuals unit by unit for 107 arrays...done
20110921 10:16:35| Calculating FIRMA scores...
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