R Bioconductor package Affxparser keeps crashing
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Entering edit mode
Cameron • 0
@dc3fc641
Last seen 8 weeks ago
United States

I am currently working on getting data from .chp files into a table. I am using the R Bioconductor package affxparser to do this. However, it keeps crashing before the data will download. If you could take a look at my code below and give me any advice I would really appreciate it!

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

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

BiocManager::install("affxparser")

library("affxparser")


There is no output since it just keeps crashing. The data I used is public and can be downloaded at this website:https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM2252974. Go to the bottom of the page and download GSM2252974_6181.sst-rma-gene-full.chp.gz, ftp, CHP version.

Thank you in advance for any and all help!

affxparser r Bioconductor • 155 views
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Entering edit mode

Not really an answer on how to solve your problem, but when I quickly checked on my system it turns out your lines of code are working as expected.... So it must be something specific to your system I guess.

>  library(affxparser)
> class(data)
[1] "list"
$FileId [1] "0000008197-1443449417-0000025614-0000025462-0000000179"$AlgorithmName
[1] "sst-rma-gene-full"

$AlgorithmVersion [1] "1.0"$ArrayType
[1] "MTA-1_0"

$AlgorithmParameters$AlgorithmParameters$apt-engine [1] "ProbesetSummarizeEngine"$AlgorithmParameters$apt-program-name [1] "Expression Console"$AlgorithmParameters$apt-exec-guid [1] "0000008197-1443448609-0000013569-0000021381-0000017041"$AlgorithmParameters$apt-analysis-guid [1] "00000fbf-5a75-4488-0a1b-0046a8005f24"$AlgorithmParameters$apt-time-str [1] "Mon Sep 28 09:56:50 2015" <<snip>> > sessionInfo() R version 4.2.0 Patched (2022-05-12 r82348 ucrt) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 10 x64 (build 19042) Matrix products: default Random number generation: RNG: Mersenne-Twister Normal: Inversion Sample: Rounding locale: [1] LC_COLLATE=English_United Kingdom.utf8 [2] LC_CTYPE=English_United Kingdom.utf8 [3] LC_MONETARY=English_United Kingdom.utf8 [4] LC_NUMERIC=C [5] LC_TIME=English_United Kingdom.utf8 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] affxparser_1.68.1 loaded via a namespace (and not attached): [1] compiler_4.2.0 >  ADD REPLY 0 Entering edit mode @james-w-macdonald-5106 Last seen 3 hours ago United States This works for me. > library(affxparser) > library(GEOquery) > getGEOSuppFiles("GSE84876") trying URL 'https://ftp.ncbi.nlm.nih.gov/geo/series/GSE84nnn/GSE84876/suppl//GSE84876_RAW.tar?tool=geoquery' Content type 'application/x-tar' length 302858240 bytes (288.8 MB) downloaded 288.8 MB size isdir mode C:/Users/jmacdon/Desktop/GSE84876/GSE84876_RAW.tar 302858240 FALSE 666 mtime C:/Users/jmacdon/Desktop/GSE84876/GSE84876_RAW.tar 2022-06-10 11:35:39 ctime C:/Users/jmacdon/Desktop/GSE84876/GSE84876_RAW.tar 2022-06-10 11:26:34 atime exe C:/Users/jmacdon/Desktop/GSE84876/GSE84876_RAW.tar 2022-06-10 11:35:39 no > setwd("GSE84876/") > untar("GSE84876_RAW.tar") ## uncompress > sapply(dir(".", "chp.gz$"), function(x) system(paste("gzip -d", x)))
GSM2252974_6181.sst-rma-gene-full.chp.gz
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GSM2252975_6185.sst-rma-gene-full.chp.gz
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GSM2252976_6186.sst-rma-gene-full.chp.gz
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GSM2252977_6171.sst-rma-gene-full.chp.gz
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GSM2252978_6174.sst-rma-gene-full.chp.gz
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GSM2252979_6180.sst-rma-gene-full.chp.gz
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GSM2252980_6196.sst-rma-gene-full.chp.gz
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GSM2252981_6197.sst-rma-gene-full.chp.gz
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GSM2252982_6208.sst-rma-gene-full.chp.gz
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GSM2252983_6225.sst-rma-gene-full.chp.gz
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GSM2252984_6227.sst-rma-gene-full.chp.gz
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GSM2252985_6232.sst-rma-gene-full.chp.gz
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## try reading a couple of them
## now read all of them
> zlst <- lapply(dir(".", "chp\$"), readChp)


It's possible that you got a corrupted file when you downloaded directly?