Hi,
I'll leave the details to FIRMA experts, but you are using really
large values of argument 'ram'. It might be that you ran out of
memory (the you got an error message). If you used cut'n'paste,
instead of source(), to do the analysis, it might be that one of the
fit() methods was preemptively finished. If so, not all units have
been fitted. Rerun with ram=1 to see if you get a different result;
the units already fitted will be skipped.
I'm also not sure if
431210/(1190297*107)
[1] 0.003385710
is an exceptionally large fraction. Note also that 431210/107 is
exactly 4030; it could be that it is the exact same 4030 units that
are NA in all samples. That could be explained by some units are not
fitted or are Affymetrix control units.
BTW, not all methods take argument 'ram'. Instead, use the global
aroma settings for achieving the same, e.g. setOption(aromaSettings,
memory/ram, 50). More info at http://aroma-project.org/settings.
This way your scripts are clean and can be ran as-is on other
machines with less memory.
Maybe this helps(?)
/Henrik
On Mon, Aug 2, 2010 at 7:24 PM, Adi Tarca ata...@med.wayne.edu wrote:
Hi all,
I have a batch of 107 mice exon arrays for which I computed FIRMA
scores and I got many NaN, Inf and 0 values which disable further
analysis based on log FIRMA values for some probesets. I was wondering
if this is a known issue or I am the only one to get these results.
Here is the code I use to get the FIRMA scores:
library(aroma.affymetrix)
verbose - Arguments$getVerbose(-8, timestamp=TRUE)
chipType - MoEx-1_0-st-v1
cdf - AffymetrixCdfFile$byChipType(chipType,
tags=fullR1,A20080718,MR)
cs - AffymetrixCelSet$byName(mice2010, cdf=cdf)
bc - RmaBackgroundCorrection(cs, tag=fullR1,A20080718,MR)
csBC - process(bc,verbose=verbose,ram=500)
qn - QuantileNormalization(csBC, typesToUpdate=pm)
csN - process(qn, verbose=verbose,ram=500)
plmTr - ExonRmaPlm(csN, mergeGroups=TRUE)
fit(plmTr, verbose=verbose,ram=500)
firma - FirmaModel(plmTr)
fit(firma, verbose=verbose,ram=500)
fs - getFirmaScores(firma)
myres2=extractDataFrame(fs,addNames=FALSE)
myres=as.matrix(myres2[,-(1:3)])
Here is the counts of NaN Inf and 0 values:
dim(myres)
[1] 1190297 107
sum(is.nan(myres))
[1] 431210
sum(is.infinite(myres),na.rm=TRUE)
[1] 855
sum(myres==0,na.rm=TRUE)
[1] 214
R version 2.11.0 (2010-04-22)
x86_64-unknown-linux-gnu
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods
base
other attached packages:
[1] aroma.affymetrix_1.5.0 aroma.apd_0.1.7
affxparser_1.20.0
[4] R.huge_0.2.0 aroma.core_1.5.0
aroma.light_1.16.0
[7] matrixStats_0.2.1 R.rsp_0.3.6
R.cache_0.3.0
[10] R.filesets_0.8.1 digest_0.4.2
R.utils_1.4.0
[13] R.oo_1.7.2 R.methodsS3_1.2.0
--
When reporting problems on aroma.affymetrix, make sure 1) to run the latest
version of the package, 2) to report the output of sessionInfo() and
traceback(), and 3) to post a complete code example.
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--
When reporting problems on aroma.affymetrix, make sure 1) to run the latest
version of the package, 2) to report the output of sessionInfo() and
traceback(), and 3) to post a complete code example.
You received this message because you are subscribed to the Google Groups
aroma.affymetrix group with website http://www.aroma-project.org/.
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