Question

Annotating [HuGene-1_0-st] Affymetrix Human Gene 1.0 ST Array [transcript (gene) version] file

1

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kiera.lee ▴ 10

@kieralee-24324

Last seen 4.1 years ago

Hi there,

I am trying to annotate a [HuGene-1_0-st] Affymetrix Human Gene 1.0 ST Array [transcript (gene) version] file in affylmGUI. I downloaded the

if (!requireNamespace("BiocManager", quietly = TRUE)) + install.packages("BiocManager")

BiocManager::install("hugene10stv1cdf")

but it says it is not available for R 4.0.2?

Any suggestions would be appreciated!

EDIT: these are the specific warnings I get:

library(hugene10stv1cdf) Warning messages: 1: X11 protocol error: RenderBadPicture (invalid Picture parameter) 2: package ‘hugene10stv1.db’ is not available (for R version 4.0.2) 3: package ‘hugene10stv1.db’ is not available (for R version 4.0.2)

Thanks,

Kiera

microarray annotation affy • 2.8k views

ADD COMMENT • link 4.1 years ago kiera.lee ▴ 10

score 0 · Answer 1 · 2020-10-10

0

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Martin Morgan 25k

@martin-morgan-1513

Last seen 4 months ago

United States

Be sure that you are using the right version of Bioconductor for your version of R, e.g., does

BiocManager::version()

report Bioconductor version 3.11 or 3.12? If not, remove the 'BiocVersion' package

remove.packages("BiocVersion")  # repeat until all instances removed

and install again

BiocManager::install(version = "3.11")

ADD COMMENT • link 4.1 years ago Martin Morgan 25k

0

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Hi,

thanks for your response! If i do that I get,

BiocManager::version() [1] ‘3.11’

so I believe I am using the right version .

ADD REPLY • link 4.1 years ago kiera.lee ▴ 10

0

Entering edit mode

Can you provide a more complete transcript, e.g,. I have

> BiocManager::install("hugene10stv1cdf")
Bioconductor version 3.11 (BiocManager 1.30.10), R 4.0.2 Patched (2020-09-15
  r79213)
Installing package(s) 'hugene10stv1cdf'
trying URL 'https://bioconductor.org/packages/3.11/data/annotation/src/contrib/hugene10stv1cdf_2.18.0.tar.gz'
Content type 'application/x-gzip' length 3010458 bytes (2.9 MB)
==================================================
downloaded 2.9 MB

* installing *source* package 'hugene10stv1cdf' ...
** using staged installation
** R
** data
** byte-compile and prepare package for lazy loading
Warning: replacing previous import 'AnnotationDbi::tail' by 'utils::tail' when loading 'hugene10stv1cdf'
Warning: replacing previous import 'AnnotationDbi::head' by 'utils::head' when loading 'hugene10stv1cdf'
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
Warning: replacing previous import 'AnnotationDbi::tail' by 'utils::tail' when loading 'hugene10stv1cdf'
Warning: replacing previous import 'AnnotationDbi::head' by 'utils::head' when loading 'hugene10stv1cdf'
** testing if installed package can be loaded from final location
Warning: replacing previous import 'AnnotationDbi::tail' by 'utils::tail' when loading 'hugene10stv1cdf'
Warning: replacing previous import 'AnnotationDbi::head' by 'utils::head' when loading 'hugene10stv1cdf'
** testing if installed package keeps a record of temporary installation path
* DONE (hugene10stv1cdf)

The downloaded source packages are in
    '/private/var/folders/yn/gmsh_22s2c55v816r6d51fx1tnyl61/T/RtmpTpeyRi/downloaded_packages'

ADD REPLY • link 4.1 years ago Martin Morgan 25k