Trouble with gcrma, Segfault on background correction
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tangboyun ▴ 30
@tangboyun-6933
Last seen 5.3 years ago
China

Dear list,

I try to run gcrma using the affinity computation without taking into account MM probes, and following commands lead to segfault.

 

> library(simpleaffy)

> rawData <- ReadAffy() # Read in PrimeView CELs (no MM probes)

> eset <- gcrma(rawData, affinity.info=compute.affinities2(cdfName(rawData)))

Adjusting for non-specific binding.
 *** caught segfault ***
address 0x2116d0850, cause 'memory not mapped'

Traceback:
 1: runmed(x[O], 21)
 2: bg.parameters.ns(mms[index.affinities], amm, apm)
 3: bg.adjust.fullmodel(pms[, i], mms[, i], ncs = ncs[, i], apm = pm.affinities,     amm = mm.affinities, anc = anc, index.affinities, k = k,     rho = rho, fast = fast)
 4: gcrma.engine(pms = pm(object), mms = mm(object), ncs, pm.affinities = pm(affinity.info),     mm.affinities = mm(affinity.info), anc, type = type, k = k,     stretch = stretch, correction = correction, GSB.adjust = GSB.adjust,     rho = rho, verbose = verbose, fast = fast)
 5: bg.adjust.gcrma(object, affinity.info = affinity.info, affinity.source = affinity.source,     NCprobe = NCprobe, type = type, k = k, stretch = stretch,     correction = correction, GSB.adjust = GSB.adjust, rho = rho,     optical.correct = optical.correct, verbose = verbose, fast = fast)
 6: gcrma(rawData, affinity.info = compute.affinities2(cdfName(rawData)))

> sessionInfo()
R version 3.1.1 (2014-07-10)
Platform: x86_64-unknown-linux-gnu (64-bit)

locale:
 [1] LC_CTYPE=zh_CN.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=zh_CN.UTF-8        LC_COLLATE=zh_CN.UTF-8    
 [5] LC_MONETARY=zh_CN.UTF-8    LC_MESSAGES=zh_CN.UTF-8   
 [7] LC_PAPER=zh_CN.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=zh_CN.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] parallel  stats     graphics  grDevices utils     datasets  methods  
[8] base     

other attached packages:
[1] simpleaffy_2.42.0   gcrma_2.38.0        genefilter_1.48.1  
[4] affy_1.44.0         Biobase_2.26.0      BiocGenerics_0.12.0

loaded via a namespace (and not attached):
 [1] affyio_1.34.0         annotate_1.44.0       AnnotationDbi_1.28.0 
 [4] BiocInstaller_1.16.0  Biostrings_2.34.0     DBI_0.3.1            
 [7] GenomeInfoDb_1.2.2    IRanges_2.0.0         preprocessCore_1.28.0
[10] RSQLite_1.0.0         S4Vectors_0.4.0       splines_3.1.1        
[13] stats4_3.1.1          survival_2.37-7       XML_3.98-1.1         
[16] xtable_1.7-4          XVector_0.6.0         zlibbioc_1.12.0      

 

 

gcrma affy • 1.0k views
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@james-w-macdonald-5106
Last seen 1 hour ago
United States

For PM-only arrays you have to specify the NCprobes that you want to use. The primeview array doesn't really have any negative control probes, so this can be a bit problematic. There are the ERCC probes, and if you didn't use the ERCC spike in cDNA, then you could hypothetically use those.

ind <- grep("ERCC", featureNames(rawData), value = TRUE)
eset <- gcrma(rawData, affinity.info=compute.affinities2(cdfName(rawData)), NCprobe = ind, type = "affinities")
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You are right. Thank you very much. 

By the way, I found a list of probes in the primeview array design and also a paper (http://europepmc.org/articles/PMC3683922) using thses probes for bg ctrl. 

 [1] "AFFX-BkGr-GC03_at" "AFFX-BkGr-GC04_at" "AFFX-BkGr-GC05_at"
 [4] "AFFX-BkGr-GC06_at" "AFFX-BkGr-GC07_at" "AFFX-BkGr-GC08_at"
 [7] "AFFX-BkGr-GC09_at" "AFFX-BkGr-GC10_at" "AFFX-BkGr-GC11_at"
[10] "AFFX-BkGr-GC12_at" "AFFX-BkGr-GC13_at" "AFFX-BkGr-GC14_at"
[13] "AFFX-BkGr-GC15_at" "AFFX-BkGr-GC16_at" "AFFX-BkGr-GC17_at"
[16] "AFFX-BkGr-GC18_at" "AFFX-BkGr-GC19_at" "AFFX-BkGr-GC20_at"
[19] "AFFX-BkGr-GC21_at" "AFFX-BkGr-GC22_at" "AFFX-BkGr-GC23_at"
[22] "AFFX-BkGr-GC24_at" "AFFX-BkGr-GC25_at"

 

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Nice! I grepped out the AFFX probes, but didn't see those. Thanks for the update.

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Hi Jim,

I have tried out that solution but it does not work for me. What I do:

raw <- ReadAffy()

ind <- grep("ERCC", featureNames(raw), value = TRUE)

ind2 <- grep("AFFX", featureNames(raw), value = TRUE)

eset <- gcrma(raw, affinity.info=compute.affinities2(cdfName(raw)), NCprobe = union(ind, ind2), type = "affinities")

With the following error:

Adjusting for optical effect...............Done.
Computing affinities.Done.
Error in intensity(affinity.info)[NCprobe, ] :
  no 'dimnames' attribute  for array

and the warning:

xy2i is deprecated and will be removed in the next BioC release.
Use xy2indices in the affy package instead.

I am using primeview arrays, too, and primeviewcdf, primeviewprobe and the annotation library are installed. I would appreciate any hint on this issue, I can't find any solution.

 

Thanks in advance

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