Error in .local(expr, gset.idx.list, ...) : Please install the nnotation package hgu95a, but I can't install hgu95a
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yaoxucpu • 0
@yaoxucpu-24035
Last seen 4.3 years ago

I follow the GSVA guide, but I was trapped by hgu95a, I am confused, why I can only install hgu95a.db, but not hgu95a, which is necessary for GSVA analysis. Thanks for any suggestion.

cache(leukemia_es <- gsva(leukemia_filtered_eset, c2BroadSets, min.sz=10, max.sz=500, verbose=TRUE), dir=cacheDir, prefix=cachePrefix)
Error in .local(expr, gset.idx.list, ...) : 
  Please install the nnotation package hgu95a

BiocManager::install("hgu95a")
Bioconductor version 3.11 (BiocManager 1.30.10), R 4.0.2
  (2020-06-22)
Installing package(s) 'hgu95a'
Warning message:
package ‘hgu95a’ is not available (for R version 4.0.2)
GSVA • 3.0k views
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soudayo ▴ 10
@8a9dac50
Last seen 3.3 years ago
Hong Kong

Kevin Blighe's code works fine for me, but I have the same error when I run leukemia_es <- gsva(leukemia_eset, c2BroadSets, min.sz=10, max.sz=500) from vignettes of GSVA. I change the annotation of leukemia_eset into "hgu95a.db" and solve the problem.

leukemia_eset@annotation <- "hgu95a.db"

Maybe this works for you?
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Kevin Blighe ★ 4.0k
@kevin
Last seen 26 days ago
Republic of Ireland

Hey yaoxucpu,

The required package is hgu95a.db, and it should automatically be installed / loaded with the GSVAdata package.

To clarify: the GSVA error message is saying that you need to load the annotation package for the Affymetrix array platform 'hgu95a', and the package in Bioconductor for this is hgu95a.db: https://bioconductor.org/packages/release/data/annotation/html/hgu95a.db.html

The following sequence of commands runs okay for me:

library(GSEABase)
library(GSVAdata)
data(c2BroadSets)
library(Biobase)
library(genefilter)
library(limma)
library(RColorBrewer)
library(GSVA)

cacheDir <- system.file("extdata", package="GSVA")
cachePrefix <- "cache4vignette_"

data(leukemia)
leukemia_eset

filtered_eset <- nsFilter(leukemia_eset, require.entrez=TRUE, remove.dupEntrez=TRUE,
  var.func=IQR, var.filter=TRUE, var.cutoff=0.5, filterByQuantile=TRUE,
  feature.exclude="^AFFX")

cache(leukemia_es <- gsva(leukemia_filtered_eset, c2BroadSets,
  min.sz=10, max.sz=500, verbose=TRUE),
  dir=cacheDir, prefix=cachePrefix)

Kevin
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I installed hgu95a.db successfully but I'm still getting the same error message when I run your code.

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Okay, can you please show the output from the commands in my answer?

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ExpressionSet (storageMode: lockedEnvironment)
assayData: 12626 features, 37 samples
  element names: exprs
protocolData
  sampleNames: CL2001011101AA.CEL CL2001011102AA.CEL ... CL2001011152AA.CEL (37 total)
  varLabels: ScanDate
  varMetadata: labelDescription
phenoData
  sampleNames: CL2001011101AA.CEL CL2001011102AA.CEL ... CL2001011152AA.CEL (37 total)
  varLabels: subtype
  varMetadata: labelDescription channel
featureData: none
experimentData: use 'experimentData(object)'
Annotation: hgu95a
Error in .local(expr, gset.idx.list, ...) : 
  Please install the nnotation package hgu95a
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That's not the output of all commands. So, if, for whatever reason(s), you cannot post the output of all commands, what is the output of:

library(GSVAdata)

If loaded successfully, this should, in addition, load hgu95a.db and org.Hs.eg.db

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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 objects are masked from 'package:stats':

IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

anyDuplicated, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find, get, grep, grepl, intersect, is.unsorted,
lapply, Map, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank, rbind, Reduce, rownames, sapply, setdiff, sort, table, tapply, union,
unique, unsplit, which.max, which.min

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")'.

Loading required package: annotate Loading required package: AnnotationDbi Loading required package: stats4 Loading required package: IRanges Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

expand.grid

Attaching package: 'IRanges'

The following object is masked from 'package:grDevices':

windows

Loading required package: XML Loading required package: graph

Attaching package: 'graph'

The following object is masked from 'package:XML':

addNode

Loading required package: hgu95a.db Loading required package: org.Hs.eg.db

Attaching package: 'limma'

The following object is masked from 'package:BiocGenerics':

plotMA

ExpressionSet (storageMode: lockedEnvironment) assayData: 12626 features, 37 samples element names: exprs protocolData sampleNames: CL2001011101AA.CEL CL2001011102AA.CEL ... CL2001011152AA.CEL (37 total) varLabels: ScanDate varMetadata: labelDescription phenoData sampleNames: CL2001011101AA.CEL CL2001011102AA.CEL ... CL2001011152AA.CEL (37 total) varLabels: subtype varMetadata: labelDescription channel featureData: none experimentData: use 'experimentData(object)' Annotation: hgu95a Error in .local(expr, gset.idx.list, ...) : Please install the nnotation package hgu95a

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I think the problem is that the annotation slot in ExpressionSet objects trims off the extension .db from the package name that contains the annotation. So, when the software tells you to install the package hgu95a, you should actually try to install hgu95a.db, so please try the following:

BiocManager::install("hgu95a.db")
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I did install it but still no luck, although it works fine on a different machine.

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I'm currently experiencing the same error message that you're having while working through the GSVA vignette even after installing the "hgu95a.db" package with BiocManager. Here is the output of the code block you posted:

library(GSEABase)
library(GSVAdata)
data(c2BroadSets)
library(Biobase)
library(genefilter)
library(limma)
library(RColorBrewer)
library(GSVA)

cacheDir <- system.file("extdata", package="GSVA")
cachePrefix <- "cache4vignette_"

data(leukemia)
leukemia_eset

filtered_eset <- nsFilter(leukemia_eset, require.entrez=TRUE, remove.dupEntrez=TRUE,
  var.func=IQR, var.filter=TRUE, var.cutoff=0.5, filterByQuantile=TRUE,
  feature.exclude="^AFFX")

leukemia_filtered_eset <- filtered_eset$eset

cache(leukemia_es <- gsva(leukemia_filtered_eset, c2BroadSets,
  min.sz=10, max.sz=500, verbose=TRUE),
  dir=cacheDir, prefix=cachePrefix)

Results:

ExpressionSet (storageMode: lockedEnvironment)
assayData: 12626 features, 37 samples 
  element names: exprs 
protocolData
  sampleNames: CL2001011101AA.CEL CL2001011102AA.CEL ...
    CL2001011152AA.CEL (37 total)
  varLabels: ScanDate
  varMetadata: labelDescription
phenoData
  sampleNames: CL2001011101AA.CEL CL2001011102AA.CEL ...
    CL2001011152AA.CEL (37 total)
  varLabels: subtype
  varMetadata: labelDescription channel
featureData: none
experimentData: use 'experimentData(object)'
Annotation: hgu95a 
Error in .local(expr, gset.idx.list, ...): Please install the nnotation package hgu95a
Traceback:

1. cache(leukemia_es <- gsva(leukemia_filtered_eset, c2BroadSets, 
 .     min.sz = 10, max.sz = 500, verbose = TRUE), dir = cacheDir, 
 .     prefix = cachePrefix)
2. assign(name, eval(RHS, envir = parent.frame()), envir = parent.frame())
3. eval(RHS, envir = parent.frame())
4. eval(RHS, envir = parent.frame())
5. gsva(leukemia_filtered_eset, c2BroadSets, min.sz = 10, max.sz = 500, 
 .     verbose = TRUE)
6. gsva(leukemia_filtered_eset, c2BroadSets, min.sz = 10, max.sz = 500, 
 .     verbose = TRUE)
7. .local(expr, gset.idx.list, ...)
8. stop(sprintf("Please install the nnotation package %s", annotpkg))
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Hi, that's so strange. I run the same code and have no errors. Here is the output, and my sessionInfo():

leukemia_eset
ExpressionSet (storageMode: lockedEnvironment)
assayData: 12626 features, 37 samples 
  element names: exprs 
protocolData
  sampleNames: CL2001011101AA.CEL CL2001011102AA.CEL ...
    CL2001011152AA.CEL (37 total)
  varLabels: ScanDate
  varMetadata: labelDescription
phenoData
  sampleNames: CL2001011101AA.CEL CL2001011102AA.CEL ...
    CL2001011152AA.CEL (37 total)
  varLabels: subtype
  varMetadata: labelDescription channel
featureData: none
experimentData: use 'experimentData(object)'
Annotation: hgu95a 

sessionInfo()
R version 4.0.3 (2020-10-10)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.7 LTS

Matrix products: default
BLAS:   /usr/lib/atlas-base/atlas/libblas.so.3.0
LAPACK: /usr/lib/atlas-base/atlas/liblapack.so.3.0

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

attached base packages:
[1] stats4    parallel  stats     graphics  grDevices utils     datasets 
[8] methods   base     

other attached packages:
 [1] GSVA_1.36.3          RColorBrewer_1.1-2   limma_3.44.3        
 [4] genefilter_1.70.0    GSVAdata_1.24.0      hgu95a.db_3.2.3     
 [7] org.Hs.eg.db_3.11.4  GSEABase_1.50.1      graph_1.66.0        
[10] annotate_1.66.0      XML_3.99-0.5         AnnotationDbi_1.53.0
[13] IRanges_2.22.2       S4Vectors_0.26.1     Biobase_2.48.0      
[16] BiocGenerics_0.34.0 

loaded via a namespace (and not attached):
 [1] SummarizedExperiment_1.18.2 splines_4.0.3              
 [3] lattice_0.20-41             vctrs_0.3.6                
 [5] htmltools_0.5.1.1           blob_1.2.1                 
 [7] survival_3.2-7              rlang_0.4.10               
 [9] later_1.1.0.1               DBI_1.1.1                  
[11] BiocParallel_1.22.0         bit64_4.0.5                
[13] matrixStats_0.57.0          GenomeInfoDbData_1.2.3     
[15] lifecycle_0.2.0             zlibbioc_1.34.0            
[17] memoise_2.0.0               fastmap_1.1.0              
[19] httpuv_1.5.5                GenomeInfoDb_1.24.2        
[21] Rcpp_1.0.6                  xtable_1.8-4               
[23] promises_1.1.1              cachem_1.0.1               
[25] DelayedArray_0.14.1         XVector_0.28.0             
[27] mime_0.9                    bit_4.0.4                  
[29] digest_0.6.27               shiny_1.6.0                
[31] GenomicRanges_1.40.0        grid_4.0.3                 
[33] tools_4.0.3                 bitops_1.0-6               
[35] magrittr_2.0.1              shinythemes_1.2.0          
[37] RCurl_1.98-1.2              RSQLite_2.2.3              
[39] pkgconfig_2.0.3             ellipsis_0.3.1             
[41] Matrix_1.3-2                R6_2.5.0                   
[43] compiler_4.0.3

Can you clarify your system setup?

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