Question: Human Exon: arome.affymetrix residuals Inf value
0
gravatar for GENOMIC_region
7 months ago by
GENOMIC_region0 wrote:

Hello all,

I'm working HuEx ST 1.0 microarray data. Trying to get estimates for exon and transcript level, plot residuals. In the code below I perform RMA for exons. In the end I get a data frame, which looks OK. Code and steps from http://www.aroma-project.org/vignettes/FIRMA-HumanExonArrayAnalysis/

However, I'd like to plot residuals, which unfortunately fails because all the values I get are Inf. Can anyone help me figure this? 

https://groups.google.com/forum/#!forum/aroma-affymetrix Groups is inactive since long.

library("aroma.affymetrix")
cdf <- AffymetrixCdfFile$byChipType("HuEx-1_0-st-v2", tags="coreR3,A20071112,EP")
print(cdf)
cs <- AffymetrixCelSet$byName("celFiles", cdf=cdf) # rawdata in cwd. HuEx-1_0-st-v2 in celfiles # this should match cdf file names too
print(cs)
setCdf(cs, cdf)
bc <- RmaBackgroundCorrection(cs)
qn <- QuantileNormalization(csBC, typesToUpdate="pm")
csN <- process(qn)
plmTr <- ExonRmaPlm(csN, mergeGroups=FALSE)
print(plmTr)
fit(plmTr, verbose=verbose)
cesTr <- getChipEffectSet(plmTr)
trFitJJ <- extractDataFrame(cesTr, units=1:3, addNames=TRUE)
#--I get data frame with values and. Looks fine

rs <- calculateResidualSet(plmTr, verbose=verbose)
readUnits(rs) #-- this gives Inf for all the probes.

R session info below
###
R version 3.4.3 (2017-11-30)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 17134)
Matrix products: default
locale:
[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252    LC_MONETARY=English_United States.1252 LC_NUMERIC=C                           LC_TIME=English_United States.1252   
attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base    
other attached packages:
[1] preprocessCore_1.40.0  png_0.1-7              R.rsp_0.43.0           aroma.light_3.8.0      aroma.affymetrix_3.1.1 aroma.core_3.1.3       R.devices_2.16.0       R.filesets_2.12.1      R.utils_2.7.0          R.oo_1.22.0          
[11] affxparser_1.50.0      R.methodsS3_1.7.1    
loaded via a namespace (and not attached):
[1] DNAcopy_1.52.0       zlibbioc_1.24.0      BiocGenerics_0.24.0  aroma.apd_0.6.0      R.cache_0.13.0       globals_0.12.4       tools_3.4.3          parallel_3.4.3       Biobase_2.38.0       R.huge_0.9.0         affy_1.56.0        
[12] PSCBS_0.64.0         matrixStats_0.54.0   digest_0.6.18        affyio_1.48.0        base64enc_0.1-3      codetools_0.2-15     future.apply_1.0.1   BiocInstaller_1.28.0 compiler_3.4.3       future_1.10.0        listenv_0.7.0      
[23] Cairo_1.5-9         

 

 

 

exon array analysis exons • 181 views
ADD COMMENTlink modified 7 months ago by James W. MacDonald50k • written 7 months ago by GENOMIC_region0
Answer: Human Exon: arome.affymetrix residuals Inf value
2
gravatar for James W. MacDonald
7 months ago by
United States
James W. MacDonald50k wrote:

The aroma.affymetrix package is a CRAN package, not Bioconductor. As you note there once was a Google group, which may have been abandoned, and I actually have not idea if Henrik still maintains this package. But either way, you should be asking about this either on R-help (r-help@r-project.org) or asking Henrik directly. I assume the email in the DESCRIPTION file for the package is up to date.

ADD COMMENTlink written 7 months ago by James W. MacDonald50k

Ah, thank you.

ADD REPLYlink written 7 months ago by GENOMIC_region0
I should note that you can fit a PLM model using the oligo package, so you might try that.
ADD REPLYlink written 7 months ago by James W. MacDonald50k
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