Question

oposSOM error and annotation question

0

Entering edit mode

Alison Ziesel ▴ 60

@alison-ziesel-2031

Last seen 9.4 years ago

United States

I've just started with the oposSOM package to identify key genes in an array study I'm analyzing for a collaborator, and I have two questions about the package. Below is my R code and the error message, along with everything oposSOM reported during its workflow. "Eset" is an expression set generated using the oligo package.

> eset.matrix <- as.matrix(eset)
> env <- opossom.new(list(dataset.name="All",
+ error.model="all.samples",
+ dim.1stLvlSom=20,
+ dim.2ndLvlSom=20,
+ geneset.analysis=TRUE,
+ spot.coresize.groupmap=5,
+ spot.threshold.groupmap=0.75,
+ pairwise.comparison.list=list(
+ list(c("1.CEL", "2.CEL", "3.CEL", "4.CEL", "5.CEL", "6.CEL", "7.CEL", "8.CEL", "9.CEL", "11.CEL", "12.CEL", "13.CEL", "14.CEL", "16.CEL", "17.CEL", "18.CEL", "19.CEL", "21.CEL", "22.CEL", "23.CEL", "24.CEL", "25.CEL", "26.CEL", "28.CEL", "30.CEL", "31.CEL", "32.CEL", "33.CEL", "34.CEL", "35.CEL", "36.CEL", "37.CEL", "38.CEL", "39.CEL", "40.CEL", "41.CEL", "42.CEL", "43.CEL", "44.CEL", "45.CEL"), c("9.CEL", "19.CEL", "33.CEL", "34.CEL", "35.CEL", "45.CEL")),
+ list(c("1.CEL", "2.CEL", "3.CEL", "4.CEL", "5.CEL", "6.CEL", "7.CEL", "8.CEL", "9.CEL", "11.CEL", "12.CEL", "13.CEL", "14.CEL", "16.CEL", "17.CEL", "18.CEL", "19.CEL", "21.CEL", "22.CEL", "23.CEL", "24.CEL", "25.CEL", "26.CEL", "28.CEL", "30.CEL", "31.CEL", "32.CEL", "33.CEL", "34.CEL", "35.CEL", "36.CEL", "37.CEL", "38.CEL", "39.CEL", "40.CEL", "41.CEL", "42.CEL", "43.CEL", "44.CEL", "45.CEL"), c("31.CEL", "32.CEL", "33.CEL", "34.CEL", "37.CEL")))))
>
> env$indata <- eset.matrix
> env$group.labels <- c(rep("A", 6), rep("B", 40), rep("C", 5))
> env$group.colors <- c(rep("black", 6), rep("red", 40), rep("green", 5))
> opossom.run(env)
[2015-06-25 17:25:16][INFO] Started: Thu 25 Jun 2015 17:25:16
[2015-06-25 17:25:16][INFO] Setting: All
[2015-06-25 17:25:16][INFO] 1SOM Dim: 20
[2015-06-25 17:25:16][INFO] 2SOM Dim: 20
[2015-06-25 17:25:30][INFO] Load Annotation Data
[2015-06-25 17:25:32][INFO] Autodetecting annotation parameters
[2015-06-25 17:25:32][WARN] Could not find valid annotation parameters.
[2015-06-25 17:25:32][WARN] Disabling geneset analysis.
[2015-06-25 17:25:32][INFO] Processing SOM
[2015-06-25 17:28:48][INFO] Remaining ~ 17 min ~ 0.3 h
[2015-06-25 17:41:03][INFO] Saving environment image: All pre.RData
[2015-06-25 17:41:13][INFO] Processing Differential Expression
[2015-06-25 17:41:13][INFO] Processing Single Genes
[2015-06-25 17:42:12][INFO] [################################################]
[2015-06-25 17:42:12][INFO] Writing: All - Results/LPE/all_samples.bmp
[2015-06-25 17:42:23][INFO] Processing Metagenes
[2015-06-25 17:42:25][INFO] [################################################]
[2015-06-25 17:42:25][INFO] Writing: All - Results/LPE/Sigma_LPE.pdf
[2015-06-25 17:42:26][INFO] Detecting Spots
[2015-06-25 17:42:28][INFO] Plotting Sample Portraits
[2015-06-25 17:42:28][INFO] Writing: All - Results/Expression Portraits.pdf
[2015-06-25 17:42:29][INFO] Writing: All - Results/Expression Portraits alternative.pdf
[2015-06-25 17:42:32][INFO] Writing: All - Results/Rank Maps.pdf
[2015-06-25 17:42:47][INFO] Processing Supporting Information
[2015-06-25 17:42:47][INFO] Writing: All - Results/Supporting Maps&Profiles/Supporting Maps.pdf
[2015-06-25 17:49:41][INFO] Writing: All - Results/Supporting Maps&Profiles/Entropy Profiles.pdf
[2015-06-25 17:49:42][INFO] Writing: All - Results/Supporting Maps&Profiles/Topology Profiles.pdf
[2015-06-25 17:49:43][INFO] Processing 2nd level Metagene Analysis
[2015-06-25 17:49:43][INFO] Writing: All - Results/2nd lvl Metagene Analysis/Similarity Analysis.pdf
[2015-06-25 17:49:47][INFO] Writing: All - Results/2nd lvl Metagene Analysis/Correlation Analysis.pdf
[2015-06-25 17:49:52][INFO] Writing: All - Results/2nd lvl Metagene Analysis/Component Analysis.pdf
[2015-06-25 17:49:59][INFO] Writing: All - Results/2nd lvl Metagene Analysis/2nd lvl SOM.pdf
[2015-06-25 17:50:00][INFO] Processing Gene Lists
[2015-06-25 17:50:00][INFO] Writing: All - Results/CSV Sheets/Gene Lists - Global/*.csv
[2015-06-25 17:52:27][INFO] Writing: All - Results/CSV Sheets/Gene Lists - Local/*.csv
[2015-06-25 17:52:56][INFO] Processing Summary Sheets (Samples)
[2015-06-25 17:52:58][INFO] Writing: All - Results/Summary Sheets - Samples/*.pdf
[2015-06-25 17:53:42][INFO] Processing Summary Sheets (Spots)
[2015-06-25 17:53:42][INFO] Writing: All - Results/Summary Sheets - Integral/*.pdf
[2015-06-25 17:53:42][INFO] Writing: All - Results/CSV Sheets/Spot Lists/*.csv
[2015-06-25 18:05:46][INFO] Processing 3rd level Spot Analysis
[2015-06-25 18:05:46][INFO] Writing: All - Results/3rd lvl Spot Analysis/Overexpression Chromosomal Eichment.pdf
[2015-06-25 18:05:46][INFO] Writing: All - Results/3rd lvl Spot Analysis/Underexpression Chromosomal Eichment.pdf
[2015-06-25 18:05:46][INFO] Writing: All - Results/3rd lvl Spot Analysis/K-Means Cluster Chromosomal Eichment.pdf
[2015-06-25 18:05:46][INFO] Writing: All - Results/3rd lvl Spot Analysis/Group Overexpression Chromosomal Eichment.pdf
[2015-06-25 18:05:46][INFO] Writing: All - Results/3rd lvl Spot Analysis/Overexpression Spot Report.pdf
[2015-06-25 18:05:47][INFO] Writing: All - Results/3rd lvl Spot Analysis/Underexpression Spot Report.pdf
[2015-06-25 18:05:47][INFO] Writing: All - Results/3rd lvl Spot Analysis/K-Means Cluster Report.pdf
[2015-06-25 18:05:47][INFO] Writing: All - Results/3rd lvl Spot Analysis/Group Overexpression Report.pdf
[2015-06-25 18:05:47][INFO] Writing: All - Results/3rd lvl Spot Analysis/Overexpression Networks.pdf
[2015-06-25 18:05:48][INFO] Writing: All - Results/3rd lvl Spot Analysis/Underexpression Networks.pdf
[2015-06-25 18:05:49][INFO] Writing: All - Results/3rd lvl Spot Analysis/K-Means Cluster Networks.pdf
[2015-06-25 18:05:50][INFO] Writing: All - Results/3rd lvl Spot Analysis/Group Overexpression Networks.pdf
[2015-06-25 18:05:50][INFO] Generating HTML Report
[2015-06-25 18:05:50][INFO] Writing: All - Results/Summary.html
[2015-06-25 18:05:50][INFO] Writing: All - Results/Summary Sheets - Samples/0verview.html
[2015-06-25 18:05:50][INFO] Writing: All - Results/Summary Sheets - Integral/0verview.html
[2015-06-25 18:05:50][INFO] Saving environment image: All.RData
[2015-06-25 18:06:12][INFO] Processing Group-centered Analyses
[2015-06-25 18:06:12][INFO] Writing: All - Results/Summary Sheets - Groups/Expression Portraits Groups.pdf
[2015-06-25 18:06:13][INFO] Writing: All - Results/Summary Sheets - Groups/Group Assignment.pdf
Error in group.correlations[, names(S)] : subscript out of bounds

> traceback()
9: apply(group.correlations[, names(S)], 2, which.max)
8: plot.xy(xy.coords(x, y), type = type, ...)
7: points.default(b, rep(-0.2, ncol(indata)), pch = 15, cex = 1,
       col = groupwise.group.colors[apply(group.correlations[, names(S)],
           2, which.max)])
6: points(b, rep(-0.2, ncol(indata)), pch = 15, cex = 1, col = groupwise.group.colors[apply(group.correlations[,
       names(S)], 2, which.max)])
5: fn()
4: util.call(pipeline.summarySheetsGroups, environment())
3: fn()
2: util.call(pipeline.groupAnalysis, env)
1: opossom.run(env)

First question, what caused this error? Reading the reference guide and Googling didn't turn anything up.

Second question, for the files that were correctly produced prior to the error, there is no gene ID/gene symbol annotated, despite there being columns for each of these in the output files. I assume this is connected to the "[WARN] Could not find valid annotation parameters." note, but as you'll see in my sessionInfo, I do have the annotation packages loaded (Affy Human 2.0 ST annotations). Is there an additional annotation package required by this package?

I've exceeded the character limit, I'll post sessionInfo in a followup. Sorry about that!

Thanks in advance for any insight you might have on either of these questions, it's greatly appreciated.

Alison Ziesel

software error • 1.5k views

ADD COMMENT • link updated 9.5 years ago by wirth • 0 • written 9.5 years ago by Alison Ziesel ▴ 60

0

Entering edit mode

And here's that SessionInfo.

> sessionInfo()
R version 3.1.3 (2015-03-09)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X 10.9.5 (Mavericks)

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] stats4 parallel stats graphics grDevices utils datasets methods base

other attached packages:
[1] oposSOM_1.1.1                        BiocInstaller_1.16.2                 GOstats_2.32.0
[4] graph_1.44.1                         Category_2.32.0                      GO.db_3.0.0
[7] Matrix_1.1-5                         hugene20sttranscriptcluster.db_8.2.0 org.Hs.eg.db_3.0.0
[10] annotate_1.44.0                      XML_3.98-1.1                         AnnotationDbi_1.28.2
[13] GenomeInfoDb_1.2.5                   limma_3.22.7                         pd.hugene.2.0.st_3.10.0
[16] RSQLite_0.11.4                       DBI_0.3.1                            oligo_1.30.0
[19] Biostrings_2.34.1                    XVector_0.6.0                        IRanges_2.0.1
[22] S4Vectors_0.4.0                      Biobase_2.26.0                       oligoClasses_1.28.0
[25] BiocGenerics_0.12.1

loaded via a namespace (and not attached):
[1] affxparser_1.38.0     affyio_1.34.0         AnnotationForge_1.8.2 ape_3.2               biomaRt_2.22.0
[6] bit_1.1-12            codetools_0.2-10      fastICA_1.2-0         fdrtool_1.2.14        ff_2.2-13
[11] foreach_1.4.2         genefilter_1.48.1     GenomicRanges_1.18.4 grid_3.1.3            GSEABase_1.28.0
[16] igraph_0.7.1          iterators_1.0.7       KernSmooth_2.23-14    lattice_0.20-30       nlme_3.1-120
[21] pixmap_0.4-11         preprocessCore_1.28.0 RBGL_1.42.0           RCurl_1.95-4.3        scatterplot3d_0.3-35
[26] som_0.3-5             splines_3.1.3         survival_2.38-1       tools_3.1.3           xtable_1.7-4
[31] zlibbioc_1.12.0

ADD REPLY • link 9.5 years ago Alison Ziesel ▴ 60

score 0 · Answer 1 · 2015-06-26

0

Entering edit mode

wirth • 0

@wirth-7902

Last seen 7.0 years ago

Germany

Dear Alison,

first of all, your code is fine, so I see no problems at a first gance. I rather suppose some bug in the pipeline, maybe you could provide the preliminary workspace image generated by oposSOM for debugging purpose (please contact me via e-mail).

The second problem is the annotation. There will soon be an update of the package vignette which will explain the usage of the database parameters more in detail. In general, you do not need to install any annotation database packages. The gene ids, names etc. will be downloaded using biomaRt database interface, which however requieres specification of the ensemble database used ( e.g. in your case database.dataset='hsapiens_gene_ensembl' , within the parameter list in opossom.new ) and of the ID-type represented by the rownames of your data matrix ( here: database.id.type='affy_hugene_2_0_st_v1' ).

Best, Henry

ADD COMMENT • link 9.5 years ago wirth • 0

0

Entering edit mode

Hello Henry,

Thank you so much for your quick response! I've come back to it with your suggestions, and now get the following error (R code included):

> eset.matrix <- as.matrix(eset)
>
> env <- opossom.new(list(dataset.name="M All",
+ error.model="all.samples",
+ dim.1stLvlSom=20,
+ dim.2ndLvlSom=20,
+ geneset.analysis=TRUE,
+ spot.coresize.groupmap=5,
+ spot.threshold.groupmap=0.75,
+ database.dataset='hsapiens_gene_ensembl',
+ database.id.type='affy_hugene_2_0_st_v1',
+ pairwise.comparison.list=list(
+ list(c("1.CEL", "2.CEL", "3.CEL", "4.CEL", "5.CEL", "6.CEL", "7.CEL", "8.CEL", "9.CEL", "11.CEL", "12.CEL", "13.CEL", "14.CEL", "16.CEL", "17.CEL", "18.CEL", "19.CEL", "21.CEL", "22.CEL", "23.CEL", "24.CEL", "25.CEL", "26.CEL", "28.CEL", "30.CEL", "31.CEL", "32.CEL", "33.CEL", "34.CEL", "35.CEL", "36.CEL", "37.CEL", "38.CEL", "39.CEL", "40.CEL", "41.CEL", "42.CEL", "43.CEL", "44.CEL", "45.CEL"), c(" 9.CEL", " 19.CEL", " 33.CEL", " 34.CEL", " 35.CEL", " 45.CEL")),
+ list(c("1.CEL", "2.CEL", "3.CEL", "4.CEL", "5.CEL", "6.CEL", "7.CEL", "8.CEL", "9.CEL", "11.CEL", "12.CEL", "13.CEL", "14.CEL", "16.CEL", "17.CEL", "18.CEL", "19.CEL", "21.CEL", "22.CEL", "23.CEL", "24.CEL", "25.CEL", "26.CEL", "28.CEL", "30.CEL", "31.CEL", "32.CEL", "33.CEL", "34.CEL", "35.CEL", "36.CEL", "37.CEL", "38.CEL", "39.CEL", "40.CEL", "41.CEL", "42.CEL", "43.CEL", "44.CEL", "45.CEL"), c(" 31.CEL", " 32.CEL", " 33.CEL", " 34.CEL", " 37.CEL")))))
>
> env$indata <- eset.matrix
> env$group.labels <- c(rep("A", 6), rep("B", 40), rep("C", 5))
> env$group.colors <- c(rep("black", 6), rep("red", 40), rep("green", 5))
> opossom.run(env)
[2015-07-18 17:28:24][INFO] Started: Sat 18 Jul 2015 17:28:23
[2015-07-18 17:28:24][INFO] Setting: M All
[2015-07-18 17:28:24][INFO] 1SOM Dim: 20
[2015-07-18 17:28:24][INFO] 2SOM Dim: 20
[2015-07-18 17:28:39][INFO] Load Annotation Data
[2015-07-18 17:54:46][INFO] Download of 15458 GO sets with 413510 entries
[2015-07-18 17:54:50][INFO] Filtered to 3364 GO sets with 379045 entries
[2015-07-18 17:56:30][INFO] In total 7712 gene sets to be considered in analysis
[2015-07-18 17:56:30][INFO] Processing SOM
[2015-07-18 17:59:50][INFO] Remaining ~ 17 min ~ 0.3 h
[2015-07-18 18:12:51][INFO] Saving environment image: M All pre.RData
[2015-07-18 18:13:04][INFO] Processing Differential Expression
[2015-07-18 18:13:04][INFO] Processing Single Genes
[2015-07-18 18:14:48][INFO] [################################################]
[2015-07-18 18:14:48][INFO] Writing: M All - Results/LPE/all_samples.bmp
[2015-07-18 18:15:00][INFO] Processing Metagenes
[2015-07-18 18:15:03][INFO] [################################################]
[2015-07-18 18:15:03][INFO] Writing: M All - Results/LPE/Sigma_LPE.pdf
[2015-07-18 18:15:03][INFO] Detecting Spots
[2015-07-18 18:15:06][INFO] Plotting Sample Portraits
[2015-07-18 18:15:06][INFO] Writing: M All - Results/Expression Portraits.pdf
[2015-07-18 18:15:07][INFO] Writing: M All - Results/Expression Portraits alternative.pdf
[2015-07-18 18:15:10][INFO] Writing: M All - Results/Rank Maps.pdf
[2015-07-18 18:15:25][INFO] Processing Supporting Information
[2015-07-18 18:15:25][INFO] Writing: M All - Results/Supporting Maps&Profiles/Supporting Maps.pdf
[2015-07-18 18:23:20][INFO] Writing: M All - Results/Supporting Maps&Profiles/Entropy Profiles.pdf
[2015-07-18 18:23:21][INFO] Writing: M All - Results/Supporting Maps&Profiles/Topology Profiles.pdf
[2015-07-18 18:23:22][INFO] Processing 2nd level Metagene Analysis
[2015-07-18 18:23:22][INFO] Writing: M All - Results/2nd lvl Metagene Analysis/Similarity Analysis.pdf
[2015-07-18 18:23:26][INFO] Writing: M All - Results/2nd lvl Metagene Analysis/Correlation Analysis.pdf
[2015-07-18 18:23:31][INFO] Writing: M All - Results/2nd lvl Metagene Analysis/Component Analysis.pdf
[2015-07-18 18:23:38][INFO] Writing: M All - Results/2nd lvl Metagene Analysis/2nd lvl SOM.pdf
[2015-07-18 18:23:39][INFO] Processing Geneset Analysis
[2015-07-18 18:49:23][INFO] [################################################]
[2015-07-18 18:49:23][INFO] Writing: M All - Results/Geneset Analysis/0verview Heatmaps.pdf
[2015-07-18 18:49:57][INFO] Processing Geneset Profiles and Maps
[2015-07-18 18:49:57][INFO] Writing: M All - Results/CSV Sheets/Sample GSZ scores.csv
[2015-07-18 18:49:58][INFO] Writing: M All - Results/Geneset Analysis/*.{csv,pdf}
[2015-07-18 19:22:04][INFO] [################################################]{csv,pdf}
[2015-07-18 19:22:04][INFO] Processing Cancer Hallmarks
[2015-07-18 19:24:54][INFO] Writing: M All - Results/Geneset Analysis/0verview Cancer Hallmarks.pdf
[2015-07-18 19:24:55][INFO] Processing Chromosome Expression Reports
[2015-07-18 19:27:39][INFO] [################################################]
[2015-07-18 19:27:39][INFO] Writing: M All - Results/Geneset Analysis/0verview Chromosome Expression.pdf
[2015-07-18 19:27:43][INFO] Processing Gene Lists
[2015-07-18 19:27:43][INFO] Writing: M All - Results/CSV Sheets/Gene Lists - Global/*.csv
[2015-07-18 19:33:50][INFO] Writing: M All - Results/CSV Sheets/Gene Lists - Local/*.csv
[2015-07-18 19:34:23][INFO] Writing: M All - Results/CSV Sheets/Gene Set Lists - Global/*.csv
[2015-07-18 19:34:29][INFO] Processing Summary Sheets (Samples)
[2015-07-18 19:34:31][INFO] Writing: M All - Results/Summary Sheets - Samples/*.pdf
[2015-07-18 19:37:08][INFO] Processing Summary Sheets (Spots)
[2015-07-18 19:37:08][INFO] Writing: M All - Results/Summary Sheets - Integral/*.pdf
[2015-07-18 19:37:08][INFO] Writing: M All - Results/CSV Sheets/Spot Lists/*.csv
[2015-07-18 19:52:32][INFO] Processing 3rd level Spot Analysis
[2015-07-18 19:52:32][INFO] Writing: M All - Results/3rd lvl Spot Analysis/Overexpression Chromosomal Enrichment.pdf
[2015-07-18 19:52:53][INFO] Writing: M All - Results/3rd lvl Spot Analysis/Underexpression Chromosomal Enrichment.pdf
[2015-07-18 19:53:09][INFO] Writing: M All - Results/3rd lvl Spot Analysis/K-Means Cluster Chromosomal Enrichment.pdf
[2015-07-18 19:53:27][INFO] Writing: M All - Results/3rd lvl Spot Analysis/Group Overexpression Chromosomal Enrichment.pdf
[2015-07-18 19:53:35][INFO] Writing: M All - Results/3rd lvl Spot Analysis/Overexpression Spot Report.pdf
[2015-07-18 19:53:36][INFO] Writing: M All - Results/3rd lvl Spot Analysis/Underexpression Spot Report.pdf
[2015-07-18 19:53:36][INFO] Writing: M All - Results/3rd lvl Spot Analysis/K-Means Cluster Report.pdf
[2015-07-18 19:53:36][INFO] Writing: M All - Results/3rd lvl Spot Analysis/Group Overexpression Report.pdf
[2015-07-18 19:53:37][INFO] Writing: M All - Results/3rd lvl Spot Analysis/Overexpression Networks.pdf
[2015-07-18 19:53:37][INFO] Writing: M All - Results/3rd lvl Spot Analysis/Underexpression Networks.pdf
[2015-07-18 19:53:37][INFO] Writing: M All - Results/3rd lvl Spot Analysis/K-Means Cluster Networks.pdf
[2015-07-18 19:53:38][INFO] Writing: M All - Results/3rd lvl Spot Analysis/Group Overexpression Networks.pdf
[2015-07-18 19:53:38][INFO] Generating HTML Report
[2015-07-18 19:53:38][INFO] Writing: M All - Results/Summary.html
[2015-07-18 19:53:38][INFO] Writing: M All - Results/Summary Sheets - Samples/0verview.html
[2015-07-18 19:53:38][INFO] Writing: M All - Results/Summary Sheets - Integral/0verview.html
[2015-07-18 19:53:38][INFO] Writing: M All - Results/Geneset Analysis/0verview.html
[2015-07-18 19:54:44][INFO] Saving environment image: M All.RData
[2015-07-18 19:55:10][INFO] Processing Group-centered Analyses
[2015-07-18 19:55:28][INFO] Writing: M All - Results/Summary Sheets - Groups/Expression Portraits Groups.pdf
[2015-07-18 19:55:28][INFO] Writing: M All - Results/Summary Sheets - Groups/Group Assignment.pdf
Error in group.correlations[, names(S)] : subscript out of bounds

Here's the SessionInfo:

> sessionInfo()
R version 3.1.3 (2015-03-09)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X 10.9.5 (Mavericks)

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] stats4 parallel stats graphics grDevices utils datasets methods base

other attached packages:
[1] oposSOM_1.1.1                        hugene20sttranscriptcluster.db_8.2.0 org.Hs.eg.db_3.0.0
[4] annotate_1.44.0                      XML_3.98-1.1                         AnnotationDbi_1.28.2
[7] GenomeInfoDb_1.2.5                   limma_3.22.7                         pd.hugene.2.0.st_3.10.0
[10] RSQLite_0.11.4                       DBI_0.3.1                            oligo_1.30.0
[13] Biostrings_2.34.1                    XVector_0.6.0                        IRanges_2.0.1
[16] S4Vectors_0.4.0                      Biobase_2.26.0                       oligoClasses_1.28.0
[19] BiocGenerics_0.12.1

loaded via a namespace (and not attached):
[1] affxparser_1.38.0     affyio_1.34.0         ape_3.2               BiocInstaller_1.16.2 biomaRt_2.22.0
[6] bit_1.1-12            codetools_0.2-10      fastICA_1.2-0         fdrtool_1.2.14        ff_2.2-13
[11] foreach_1.4.2         GenomicRanges_1.18.4 grid_3.1.3            igraph_0.7.1          iterators_1.0.7
[16] KernSmooth_2.23-14    lattice_0.20-30       nlme_3.1-120          pixmap_0.4-11         preprocessCore_1.28.0
[21] RCurl_1.95-4.3        scatterplot3d_0.3-35 som_0.3-5             splines_3.1.3         tools_3.1.3
[26] xtable_1.7-4          zlibbioc_1.12.0

I also tried running this on a compute cluster, the error code and SessionInfo I'll include in the next comment for clarity.

Alison Ziesel

ADD REPLY • link 9.4 years ago Alison Ziesel ▴ 60

0

Entering edit mode

Attempting the same R code in a different work environment:

[2015-07-18 17:29:40][INFO] Started: Sat 18 Jul 2015 05:29:40 PM
[2015-07-18 17:29:40][INFO] Setting: Mendoza All
[2015-07-18 17:29:40][INFO] 1SOM Dim: 20
[2015-07-18 17:29:40][INFO] 2SOM Dim: 20
[2015-07-18 17:29:51][INFO] Load Annotation Data
[2015-07-18 17:54:42][INFO] Download of 15458 GO sets with 413510 entries
[2015-07-18 17:54:47][INFO] Filtered to 3364 GO sets with 379045 entries
[2015-07-18 17:56:11][INFO] In total 7712 gene sets to be considered in analysis
[2015-07-18 17:56:11][INFO] Processing SOM
[2015-07-18 17:58:36][INFO] Remaining ~ 12 min ~ 0.2 h
[2015-07-18 18:08:36][INFO] Saving environment image: Mendoza All pre.RData
[2015-07-18 18:08:43][INFO] Processing Differential Expression
[2015-07-18 18:08:43][INFO] Processing Single Genes
[2015-07-18 18:09:36][INFO] [################################################]
[2015-07-18 18:09:36][INFO] Writing: Mendoza All - Results/LPE/all_samples.bmp
[2015-07-18 18:09:49][INFO] Processing Metagenes
[2015-07-18 18:09:50][INFO] [################################################]
[2015-07-18 18:09:50][INFO] Writing: Mendoza All - Results/LPE/Sigma_LPE.pdf
[2015-07-18 18:09:50][INFO] Detecting Spots
[2015-07-18 18:09:52][INFO] Plotting Sample Portraits
[2015-07-18 18:09:52][INFO] Writing: Mendoza All - Results/Expression Portraits.pdf
[2015-07-18 18:09:53][INFO] Writing: Mendoza All - Results/Expression Portraits alternative.pdf
[2015-07-18 18:09:56][INFO] Writing: Mendoza All - Results/Rank Maps.pdf
[2015-07-18 18:10:10][INFO] Processing Supporting Information
[2015-07-18 18:10:10][INFO] Writing: Mendoza All - Results/Supporting Maps&Profiles/Supporting Maps.pdf
[2015-07-18 18:15:30][INFO] Writing: Mendoza All - Results/Supporting Maps&Profiles/Entropy Profiles.pdf
[2015-07-18 18:15:31][INFO] Writing: Mendoza All - Results/Supporting Maps&Profiles/Topology Profiles.pdf
[2015-07-18 18:15:32][INFO] Processing 2nd level Metagene Analysis
[2015-07-18 18:15:32][INFO] Writing: Mendoza All - Results/2nd lvl Metagene Analysis/Similarity Analysis.pdf
[2015-07-18 18:15:34][INFO] Writing: Mendoza All - Results/2nd lvl Metagene Analysis/Correlation Analysis.pdf
Error in .Call("R_igraph_layout_kamada_kawai", graph, coords, maxiter, :
At structural_properties.c:5235 : cannot run Bellman-Ford algorithm, Negative loop detected while calculating shortest paths
> sessionInfo()
R version 3.1.2 (2014-10-31)
Platform: x86_64-unknown-linux-gnu (64-bit)

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=en_US.UTF-8    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] stats4 parallel stats graphics grDevices utils datasets
[8] methods base

other attached packages:
[1] oposSOM_1.1.1           annotate_1.44.0         XML_3.98-1.3
[4] AnnotationDbi_1.28.2    GenomeInfoDb_1.2.5      limma_3.22.7
[7] pd.hugene.2.0.st_3.10.0 RSQLite_1.0.0           DBI_0.3.1
[10] oligo_1.30.0            Biostrings_2.34.1       XVector_0.6.0
[13] IRanges_2.0.1           S4Vectors_0.4.0         Biobase_2.26.0
[16] oligoClasses_1.28.0     BiocGenerics_0.12.1

loaded via a namespace (and not attached):
[1] affxparser_1.38.0     affyio_1.34.0         ape_3.3
[4] BiocInstaller_1.16.5 biomaRt_2.22.0        bit_1.1-12
[7] bitops_1.0-6          codetools_0.2-11      fastICA_1.2-0
[10] fdrtool_1.2.15        ff_2.2-13             foreach_1.4.2
[13] GenomicRanges_1.18.4 grid_3.1.2            igraph_1.0.1
[16] iterators_1.0.7       KernSmooth_2.23-15    lattice_0.20-31
[19] magrittr_1.5          nlme_3.1-121          pixmap_0.4-11
[22] preprocessCore_1.28.0 RCurl_1.95-4.7        scatterplot3d_0.3-35
[25] som_0.3-5             splines_3.1.2         tools_3.1.2
[28] xtable_1.7-4          zlibbioc_1.12.0

I'm puzzled that I get different error messages in different work environments. Neither one allows me to complete my analysis, unfortunately. Would you still like me to send the preliminary workspace images to you (or rather, a Dropbox link to your email)? I really appreciate your assistance with this!

Alison Ziesel

ADD REPLY • link 9.4 years ago Alison Ziesel ▴ 60