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Kostas Kerkentzes
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10
@kostas-kerkentzes-6473
Last seen 10.3 years ago
Hello list and Evarist,
I am using the phenoTest package in order to perform gene set
enrichment
analysis but I am getting some weird(I think) errors.
What I want to do is find the statistically significant enriched GO
categories and KEGG pathways of the upregulated, downregulated and
differentially expressed genes. I was able to find the enriched GO and
KEGG for the upregulated and downregulated genes using these calls of
gsea:
gseaGOResults <- gsea.go(newDiffExpr, ontologies = 'BP',
p.adjust.method='BH');
gseaKEGGResults <- gsea.kegg(newDiffExpr,
p.adjust.method='BH');
But when I do the same call with the parameter absVals set to TRUE(to
find the enriched GO and KEGG based for the differentially expressed
genes), for example I do this like this for the KEGG pathways:
gseaKEGGResults <- gsea.kegg(newDiffExpr,
p.adjust.method='BH',
absVals = TRUE);
I get the following error:
Error in gam(y.nosel ~ s(x.nosel, k = k, bs = "cr")) : Not
enough (non-NA) data to do anything meaningful
I also get another error but not always. Unfortunately, I could not
find
exactly under which circumstances each error occurred. The second
error
is this:
Error in smooth.construct.cr.smooth.spec(object, dk$data,
dk$knots) : x.nosel has insufficient unique values to support 10
knots:
reduce k.
You can find here
<https: www.dropbox.com="" s="" 7ojwm0gmjlkj2s5="" gsea_test.zip=""> my data and
a
small script of what I am running. In the end of the email I have
written also the output of sessionInfo() and traceback() of the first
error.
Am I doing something wrong or have I overlooked something?
Thank you in advance,
Kostas Kerkentzes
Postgraduate student,
Computer Science Department,
University of Crete
This is the output of sessionInfo():
R version 3.0.2 (2013-09-25)
Platform: x86_64-w64-mingw32/x64 (64-bit)
locale:
[1] LC_COLLATE=Greek_Greece.1253 LC_CTYPE=Greek_Greece.1253
LC_MONETARY=Greek_Greece.1253
[4] LC_NUMERIC=C LC_TIME=Greek_Greece.1253
attached base packages:
[1] grid splines parallel stats graphics grDevices
utils datasets methods
[10] base
other attached packages:
[1] KEGG.db_2.10.1 hgu95av2.db_2.10.1 org.Hs.eg.db_2.10.1
phenoTest_1.10.0
[5] RSQLite_0.11.4 DBI_0.2-7 gridExtra_0.9.1
ggplot2_0.9.3.1
[9] BMA_3.16.2.3 robustbase_0.90-2 leaps_2.9
survival_2.37-7
[13] Heatplus_2.8.0 annotate_1.40.1 AnnotationDbi_1.24.0
Biobase_2.22.0
[17] BiocGenerics_0.8.0
loaded via a namespace (and not attached):
[1] affy_1.40.0 affyio_1.30.0 BiocInstaller_1.12.0
biomaRt_2.18.0
[5] BioNet_1.23.2 Biostrings_2.30.1 bit_1.1-11
bitops_1.0-6
[9] Category_2.28.0 caTools_1.16 cellHTS2_2.26.0
cluster_1.15.1
[13] codetools_0.2-8 colorspace_1.2-4 DEoptimR_1.0-1
dichromat_2.0-0
[17] digest_0.6.4 ellipse_0.3-8 ff_2.2-12
foreach_1.4.1
[21] Formula_1.1-1 gdata_2.13.2 genefilter_1.44.0
GenomicRanges_1.14.4
[25] gplots_2.12.1 graph_1.40.1 GSEABase_1.24.0
gtable_0.1.2
[29] gtools_3.3.1 hgu133a.db_2.10.1 Hmisc_3.14-3
hopach_2.22.0
[33] HTSanalyzeR_2.14.0 igraph_0.7.0 IRanges_1.20.7
iterators_1.0.6
[37] KernSmooth_2.23-10 labeling_0.2 lattice_0.20-27
latticeExtra_0.6-26
[41] limma_3.18.13 MASS_7.3-30 Matrix_1.1-2-2
mgcv_1.7-28
[45] munsell_0.4.2 mvtnorm_0.9-9997 nlme_3.1-115
oligoClasses_1.24.0
[49] pcaPP_1.9-49 plyr_1.8.1 prada_1.38.0
preprocessCore_1.24.0
[53] proto_0.3-10 RankProd_2.34.0 RBGL_1.38.0
RColorBrewer_1.0-5
[57] Rcpp_0.11.0 RCurl_1.95-4.1 reshape2_1.2.2
rrcov_1.3-4
[61] scales_0.2.3 SNPchip_2.8.0 stats4_3.0.2
stringr_0.6.2
[65] tools_3.0.2 vsn_3.30.0 XML_3.98-1.1
xtable_1.7-3
[69] XVector_0.2.0 zlibbioc_1.8.0
This is the output of traceback():
13: stop("Not enough (non-NA) data to do anything meaningful")
12: gam(y.nosel ~ s(x.nosel, k = k, bs = "cr"))
11: getNesGam(escore, gsets.len, es.sim)
10: getSummary(es, es.sim, fchr, p.adjust.method = p.adjust.method,
pval.comp.method, pval.smooth.tail, signatures, test,
fewGsets)
9: cbind(n = unlist(lapply(x$s, length)), getSummary(es, es.sim,
fchr, p.adjust.method = p.adjust.method, pval.comp.method,
pval.smooth.tail, signatures, test, fewGsets))
8: gseaSignificance(x, p.adjust.method, pval.comp.method,
pval.smooth.tail)
7: gseaSignificance(x, p.adjust.method, pval.comp.method,
pval.smooth.tail)
6: FUN(X[[1L]], ...)
5: lapply(x, function(x) gseaSignificance(x, p.adjust.method,
pval.comp.method,
pval.smooth.tail))
4: gseaSignificance(sim, p.adjust.method = p.adjust.method,
pval.comp.method = pval.comp.method,
pval.smooth.tail = pval.smooth.tail)
3: gseaSignificance(sim, p.adjust.method = p.adjust.method,
pval.comp.method = pval.comp.method,
pval.smooth.tail = pval.smooth.tail)
2: gsea(x = x, gsets = kegg, logScale = logScale, absVals = absVals,
averageRepeats = averageRepeats, B = B, mc.cores = mc.cores,
test = test, p.adjust.method = p.adjust.method,
pval.comp.method = pval.comp.method,
pval.smooth.tail = pval.smooth.tail, minGenes = minGenes,
maxGenes = maxGenes, center = center)
1: gsea.kegg(newDiffExpr, p.adjust.method = "BH", absVals = TRUE)
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