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")
data<-readChp("C:/data/GSM2252974_6181.sst-rma-gene-full.chp")
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.
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)
> data <- readChp("GSM2252974_6181.sst-rma-gene-full.chp")
> class(data)
[1] "list"
> head(data)
$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
>
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.