example in vignette error #12
Comments
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Hi, I can't replicate your error. Below is a full reproducible example of the code you mentionned, as you can see I don't have your error. Please check the session information in the end. library(GEOquery)
#> Loading required package: Biobase
#> 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,
#> which.max, which.min
#> Welcome to Bioconductor
#>
#> Vignettes contain introductory material; view with
#> 'browseVignettes()'. To cite Bioconductor, see
#> 'citation("Biobase")', and for packages 'citation("pkgname")'.
#> Setting options('download.file.method.GEOquery'='auto')
#> Setting options('GEOquery.inmemory.gpl'=FALSE)
# Download data
gse <- getGEO("GSE70970")
#> Found 1 file(s)
#> GSE70970_series_matrix.txt.gz
#> Parsed with column specification:
#> cols(
#> .default = col_double(),
#> ID_REF = col_character()
#> )
#> See spec(...) for full column specifications.
#> File stored at:
#> /tmp/RtmpKA2y6S/GPL20699.soft
# Get phenotypes
targets <- pData(phenoData(gse[[1]]))
getGEOSuppFiles(GEO = "GSE70970", baseDir = tempdir())
#> size
#> /tmp/RtmpKA2y6S/GSE70970/GSE70970_RAW.tar 1986560
#> /tmp/RtmpKA2y6S/GSE70970/GSE70970_characteristics_readme.txt.gz 672
#> isdir mode
#> /tmp/RtmpKA2y6S/GSE70970/GSE70970_RAW.tar FALSE 644
#> /tmp/RtmpKA2y6S/GSE70970/GSE70970_characteristics_readme.txt.gz FALSE 644
#> mtime
#> /tmp/RtmpKA2y6S/GSE70970/GSE70970_RAW.tar 2019-11-15 11:25:23
#> /tmp/RtmpKA2y6S/GSE70970/GSE70970_characteristics_readme.txt.gz 2019-11-15 11:25:24
#> ctime
#> /tmp/RtmpKA2y6S/GSE70970/GSE70970_RAW.tar 2019-11-15 11:25:23
#> /tmp/RtmpKA2y6S/GSE70970/GSE70970_characteristics_readme.txt.gz 2019-11-15 11:25:24
#> atime
#> /tmp/RtmpKA2y6S/GSE70970/GSE70970_RAW.tar 2019-11-15 11:25:21
#> /tmp/RtmpKA2y6S/GSE70970/GSE70970_characteristics_readme.txt.gz 2019-11-15 11:25:23
#> uid gid
#> /tmp/RtmpKA2y6S/GSE70970/GSE70970_RAW.tar 1738 50
#> /tmp/RtmpKA2y6S/GSE70970/GSE70970_characteristics_readme.txt.gz 1738 50
#> uname
#> /tmp/RtmpKA2y6S/GSE70970/GSE70970_RAW.tar mcanouil
#> /tmp/RtmpKA2y6S/GSE70970/GSE70970_characteristics_readme.txt.gz mcanouil
#> grname
#> /tmp/RtmpKA2y6S/GSE70970/GSE70970_RAW.tar staff
#> /tmp/RtmpKA2y6S/GSE70970/GSE70970_characteristics_readme.txt.gz staff
# Unzip data
untar(
tarfile = paste0(tempdir(), "/GSE70970/GSE70970_RAW.tar"),
exdir = paste0(tempdir(), "/GSE70970/Data")
)
# Add IDs
targets$IDFILE <- list.files(paste0(tempdir(), "/GSE70970/Data"))
library(NACHO)
#>
#> Attaching package: 'NACHO'
#> The following object is masked from 'package:BiocGenerics':
#>
#> normalize
GSE70970_sum <- summarise(
data_directory = paste0(tempdir(), "/GSE70970/Data"), # Where the data is
ssheet_csv = targets, # The samplesheet
id_colname = "IDFILE", # Name of the column that contains the identfiers
housekeeping_genes = NULL, # Custom list of housekeeping genes
housekeeping_predict = TRUE, # Predict the housekeeping genes based on the data?
normalisation_method = "GEO", # Geometric mean or GLM
n_comp = 5 # Number indicating the number of principal components to compute.
)
#> [NACHO] Importing RCC files.
#> [NACHO] Performing QC and formatting data.
#> [NACHO] Searching for the best housekeeping genes.
#> [NACHO] Computing normalisation factors using "GEO" method for housekeeping genes prediction.
#> [NACHO] The following predicted housekeeping genes will be used for normalisation:
#> - hsa-miR-103
#> - hsa-let-7e
#> - hsa-miR-1260
#> - hsa-miR-500+hsa-miR-501-5p
#> - hsa-miR-1274b
#> [NACHO] Computing normalisation factors using "GEO" method.
#> [NACHO] Missing values have been replaced with zeros for PCA.
#> [NACHO] Normalising data using "GEO" method with housekeeping genes.
#> [NACHO] Returning a list.
#> $ access : character
#> $ housekeeping_genes : character
#> $ housekeeping_predict: logical
#> $ housekeeping_norm : logical
#> $ normalisation_method: character
#> $ remove_outliers : logical
#> $ n_comp : numeric
#> $ data_directory : character
#> $ pc_sum : data.frame
#> $ nacho : data.frame
#> $ outliers_thresholds : list
#> $ raw_counts : data.frame
#> $ normalised_counts : data.frame
sessioninfo::session_info()
#> ─ Session info ──────────────────────────────────────────────────────────
#> setting value
#> version R version 3.6.1 (2019-07-05)
#> os Debian GNU/Linux 9 (stretch)
#> system x86_64, linux-gnu
#> ui X11
#> language en_GB.UTF-8
#> collate en_US.UTF-8
#> ctype en_US.UTF-8
#> tz Etc/UTC
#> date 2019-11-15
#>
#> ─ Packages ──────────────────────────────────────────────────────────────
#> package * version date lib source
#> assertthat 0.2.1 2019-03-21 [1] CRAN (R 3.6.1)
#> backports 1.1.5 2019-10-02 [1] CRAN (R 3.6.1)
#> Biobase * 2.44.0 2019-05-02 [1] Bioconductor
#> BiocGenerics * 0.30.0 2019-05-02 [1] Bioconductor
#> cli 1.1.0 2019-03-19 [1] CRAN (R 3.6.1)
#> colorspace 1.4-1 2019-03-18 [1] CRAN (R 3.6.1)
#> crayon 1.3.4 2017-09-16 [1] CRAN (R 3.6.1)
#> curl 4.2 2019-09-24 [1] CRAN (R 3.6.1)
#> digest 0.6.21 2019-09-20 [1] CRAN (R 3.6.1)
#> dplyr 0.8.3 2019-07-04 [1] CRAN (R 3.6.1)
#> ellipsis 0.3.0 2019-09-20 [1] CRAN (R 3.6.1)
#> evaluate 0.14 2019-05-28 [1] CRAN (R 3.6.1)
#> GEOquery * 2.52.0 2019-05-02 [1] Bioconductor
#> ggplot2 3.2.1 2019-08-10 [1] CRAN (R 3.6.1)
#> glue 1.3.1 2019-03-12 [1] CRAN (R 3.6.1)
#> gtable 0.3.0 2019-03-25 [1] CRAN (R 3.6.1)
#> highr 0.8 2019-03-20 [1] CRAN (R 3.6.1)
#> hms 0.5.1 2019-08-23 [1] CRAN (R 3.6.1)
#> htmltools 0.4.0 2019-10-04 [1] CRAN (R 3.6.1)
#> knitr 1.25 2019-09-18 [1] CRAN (R 3.6.1)
#> lazyeval 0.2.2 2019-03-15 [1] CRAN (R 3.6.1)
#> lifecycle 0.1.0 2019-08-01 [1] CRAN (R 3.6.1)
#> limma 3.40.6 2019-07-26 [1] Bioconductor
#> magrittr 1.5 2014-11-22 [1] CRAN (R 3.6.1)
#> munsell 0.5.0 2018-06-12 [1] CRAN (R 3.6.1)
#> NACHO * 0.6.1 2019-10-12 [1] CRAN (R 3.6.1)
#> pillar 1.4.2 2019-06-29 [1] CRAN (R 3.6.1)
#> pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 3.6.1)
#> purrr 0.3.3 2019-10-18 [1] CRAN (R 3.6.1)
#> R6 2.4.0 2019-02-14 [1] CRAN (R 3.6.1)
#> Rcpp 1.0.2 2019-07-25 [1] CRAN (R 3.6.1)
#> readr 1.3.1 2018-12-21 [1] CRAN (R 3.6.1)
#> rlang 0.4.0 2019-06-25 [1] CRAN (R 3.6.1)
#> rmarkdown 1.16 2019-10-01 [1] CRAN (R 3.6.1)
#> scales 1.0.0 2018-08-09 [1] CRAN (R 3.6.1)
#> sessioninfo 1.1.1 2018-11-05 [1] CRAN (R 3.6.1)
#> stringi 1.4.3 2019-03-12 [1] CRAN (R 3.6.1)
#> stringr 1.4.0 2019-02-10 [1] CRAN (R 3.6.1)
#> tibble 2.1.3 2019-06-06 [1] CRAN (R 3.6.1)
#> tidyr 1.0.0 2019-09-11 [1] CRAN (R 3.6.1)
#> tidyselect 0.2.5 2018-10-11 [1] CRAN (R 3.6.1)
#> vctrs 0.2.0 2019-07-05 [1] CRAN (R 3.6.1)
#> withr 2.1.2 2018-03-15 [1] CRAN (R 3.6.1)
#> xfun 0.10 2019-10-01 [1] CRAN (R 3.6.1)
#> xml2 1.2.2 2019-08-09 [1] CRAN (R 3.6.1)
#> yaml 2.2.0 2018-07-25 [1] CRAN (R 3.6.1)
#> zeallot 0.1.0 2018-01-28 [1] CRAN (R 3.6.1)
#>
#> [1] /usr/local/lib/R/site-library
#> [2] /usr/local/lib/R/library |
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I restarted R and tried again now it worked, sry dont know what went wrong the first time. best regards
Attaching package: ‘BiocGenerics’ The following objects are masked from ‘package:parallel’: The following objects are masked from ‘package:stats’: The following objects are masked from ‘package:base’: Welcome to Bioconductor Setting options('download.file.method.GEOquery'='auto')
Parsed with column specification:
trying URL 'https://ftp.ncbi.nlm.nih.gov/geo/series/GSE70nnn/GSE70970/suppl//GSE70970_characteristics_readme.txt.gz?tool=geoquery'
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Perfect! |
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Hi Mcanouil, Restarted R and tried to run the code fresh again. Still the same error!
Error goes like this : Any other solutions? Athul |
if I follow the example in the vignette I encounter this error:
Add IDs
[NACHO] Importing RCC files.
Error: Column
colsmust be length 1 (the number of rows), not 3The text was updated successfully, but these errors were encountered: