[BioC] Error message using arrayweights
Matt Ritchie
mritchie at wehi.EDU.AU
Thu Dec 19 05:38:17 CET 2013
Dear Rich,
Thanks for the detailed example. If you send the data (offline) I can check what is going on in more detail.
My suspicion is that you have a bunch of genes with identical values across all samples which leads to a convergence issue.
You could try leaving out the arrayWeights() step, i.e.
fit<-lmFit(gcrmanm,design)
if you need results in a hurry.
Best wishes,
Matt
----- Original Message -----
From: "Richard Friedman" <friedman at c2b2.columbia.edu>
To: "bioconductor at r-project.org list" <bioconductor at r-project.org>
Sent: Thursday, 19 December, 2013 7:27:33 AM
Subject: [BioC] Error message using arrayweights
Dear List,
I got the following error message in array weights:
arrayw<-arrayWeights(gcrmanm, design, method = "genebygene", maxiter = 50, tol = 1e-10)
Error in arrayWeights(gcrmanm, design, method = "genebygene", maxiter = 50, :
convergence problem at gene 3021: array weights not estimable
Here is the whole story:
####################################################################
> library(affy)
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: ‘BiocGenerics’
The following objects are masked from ‘package:parallel’:
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport,
clusterMap, parApply, parCapply, parLapply, parLapplyLB, parRapply, parSapply,
parSapplyLB
The following object is masked from ‘package:stats’:
xtabs
The following objects are masked from ‘package:base’:
anyDuplicated, as.data.frame, cbind, colnames, duplicated, eval, Filter, Find,
get, intersect, lapply, Map, mapply, match, mget, order, paste, pmax, pmax.int,
pmin, pmin.int, Position, rank, rbind, Reduce, rep.int, rownames, sapply,
setdiff, sort, table, tapply, union, unique, unlist
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with 'browseVignettes()'. To cite
Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'.
Warning message:
'.find.package' is deprecated.
Use 'find.package' instead.
See help("Deprecated")
> library(annaffy)
Loading required package: GO.db
Loading required package: AnnotationDbi
Loading required package: DBI
Loading required package: KEGG.db
KEGG.db contains mappings based on older data because the original resource was
removed from the the public domain before the most recent update was produced. This
package should now be considered deprecated and future versions of Bioconductor may
not have it available. Users who want more current data are encouraged to look at
the KEGGREST or reactome.db packages
> library(gcrma)
> library(limma)
> library(mouse4302.db)
Loading required package: org.Mm.eg.db
> raw<-ReadAffy()
> gcrmanm<-gcrma(raw)
Adjusting for optical effect............Done.
Computing affinities.Done.
Adjusting for non-specific binding............Done.
Normalizing
Calculating Expression
> write.exprs(gcrmanm,"gloria2gcconexp.txt")
>
>
> targets<-readTargets("targets.txt")
> targets
FileName Name mouse condition
AA.het.con.01.01 AA.het.con.01.01.CEL AA.het.con.01.01 1 AA.het.con
AA.het.con.02.03 AA.het.con.02.03.CEL AA.het.con.02.03 2 AA.het.con
AA.het.con.05.09 AA.het.con.05.09.CEL AA.het.con.05.09 5 AA.het.con
AA.het.con.06.11 AA.het.con.06.11.CEL AA.het.con.06.11 6 AA.het.con
AA.het.con.11.21 AA.het.con.11.21.CEL AA.het.con.11.21 11 AA.het.con
AA.het.con.12.23 AA.het.con.12.23.CEL AA.het.con.12.23 12 AA.het.con
AB.het.sta.01.02 AB.het.sta.01.02.CEL AB.het.sta.01.02 1 AB.het.sta
AB.het.sta.02.04 AB.het.sta.02.04.CEL AB.het.sta.02.04 2 AB.het.sta
AB.het.sta.05.10 AB.het.sta.05.10.CEL AB.het.sta.05.10 5 AB.het.sta
AB.het.sta.06.12 AB.het.sta.06.12.CEL AB.het.sta.06.12 6 AB.het.sta
AB.het.sta.11.22 AB.het.sta.11.22.CEL AB.het.sta.11.22 11 AB.het.sta
AB.het.sta.12.24 AB.het.sta.12.24.CEL AB.het.sta.12.24 12 AB.het.sta
BA.mut.con.03.05 BA.mut.con.03.05.CEL BA.mut.con.03.05 3 BA.mut.con
BA.mut.con.04.07 BA.mut.con.04.07.CEL BA.mut.con.04.07 4 BA.mut.con
BA.mut.con.07.13 BA.mut.con.07.13.CEL BA.mut.con.07.13 7 BA.mut.con
BA.mut.con.08.15 BA.mut.con.08.15.CEL BA.mut.con.08.15 8 BA.mut.con
BA.mut.con.09.17 BA.mut.con.09.17.CEL BA.mut.con.09.17 9 BA.mut.con
BB.mut.con.10.19 BB.mut.con.10.19.CEL BA.mut.con.10.19 10 BA.mut.con
BB.mut.sta.03.06 BB.mut.sta.03.06.CEL BB.mut.sta.03.06 3 BB.mut.sta
BB.mut.sta.04.08 BB.mut.sta.04.08.CEL BB.mut.sta.04.08 4 BB.mut.sta
BB.mut.sta.07.14 BB.mut.sta.07.14.CEL BB.mut.sta.07.14 7 BB.mut.sta
BB.mut.sta.08.16 BB.mut.sta.08.16.CEL BB.mut.sta.08.16 8 BB.mut.sta
BB.mut.sta.09.18 BB.mut.sta.09.18.CEL BB.mut.sta.09.18 9 BB.mut.sta
BB.mut.sta.10.20 BB.mut.sta.10.20.CEL BB.mut.sta.10.20 10 BB.mut.sta
> condition<-factor(targets$condition,levels=c("AA.het.con","BA.mut.con"))
> condition
[1] AA.het.con AA.het.con AA.het.con AA.het.con AA.het.con AA.het.con <NA> <NA>
[9] <NA> <NA> <NA> <NA> BA.mut.con BA.mut.con BA.mut.con BA.mut.con
[17] BA.mut.con BA.mut.con <NA> <NA> <NA> <NA> <NA> <NA>
Levels: AA.het.con BA.mut.con
> design<-model.matrix(~0+condition)
> design
conditionAA.het.con conditionBA.mut.con
1 1 0
2 1 0
3 1 0
4 1 0
5 1 0
6 1 0
13 0 1
14 0 1
15 0 1
16 0 1
17 0 1
18 0 1
attr(,"assign")
[1] 1 1
attr(,"contrasts")
attr(,"contrasts")$condition
[1] "contr.treatment"
>
> colnames(design)<-c("AA.het.con","BA.mut.con")
>
> arrayw<-arrayWeights(gcrmanm, design, method = "genebygene", maxiter = 50, tol = 1e-10)
Error in arrayWeights(gcrmanm, design, method = "genebygene", maxiter = 50, :
convergence problem at gene 3021: array weights not estimable
> fit<-lmFit(gcrmanm,design,weights=arrayw)
Error in lm.series(y$exprs, design = design, ndups = ndups, spacing = spacing, :
object 'arrayw' not found
> sessionInfo()
R version 3.0.2 (2013-09-25)
Platform: x86_64-apple-darwin10.8.0 (64-bit)
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] parallel stats graphics grDevices utils datasets methods base
other attached packages:
[1] mouse4302probe_2.12.0 mouse4302cdf_2.12.0 mouse4302.db_2.9.0 org.Mm.eg.db_2.9.0
[5] gcrma_2.32.0 annaffy_1.32.0 KEGG.db_2.9.1 GO.db_2.9.0
[9] RSQLite_0.11.4 DBI_0.2-7 AnnotationDbi_1.22.6 affy_1.38.1
[13] Biobase_2.20.1 BiocGenerics_0.6.0 limma_3.16.8 BiocInstaller_1.10.4
loaded via a namespace (and not attached):
[1] affyio_1.28.0 Biostrings_2.28.0 IRanges_1.18.4 preprocessCore_1.22.0
[5] splines_3.0.2 stats4_3.0.2 tools_3.0.2 zlibbioc_1.6.0
>
####################################################################
When I try with reml I get the same error message:
################################################################
> arrayw<-arrayWeights(gcrmanm, design, method = "reml",maxiter = 50, tol = 1e-10)
Error in arrayWeights(gcrmanm, design, method = "reml", maxiter = 50, :
convergence problem at iteration 1: array weights not estimable
>
######################################################################
I would appreciate any suggestions.
Best wishes,
Rich
Richard A. Friedman, PhD
Associate Research Scientist,
Biomedical Informatics Shared Resource
Herbert Irving Comprehensive Cancer Center (HICCC)
Lecturer,
Department of Biomedical Informatics (DBMI)
Educational Coordinator,
Center for Computational Biology and Bioinformatics (C2B2)/
National Center for Multiscale Analysis of Genomic Networks (MAGNet)/
Columbia Department of Systems Biology
Room 824
Irving Cancer Research Center
Columbia University
1130 St. Nicholas Ave
New York, NY 10032
(212)851-4765 (voice)
friedman at c2b2.columbia.edu
http://friedman.c2b2.columbia.edu/
In memoriam, Frederik Pohl
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