R Bioconductor package Affxparser keeps crashing
1
0
Entering edit mode
Cameron • 0
@dc3fc641
Last seen 8 weeks ago
United States

Hi! Undergraduate Biomathematics student here.

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.

Thank you in advance for any and all help!

affxparser r Bioconductor • 155 views
ADD COMMENT
0
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)
> 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
>
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$"), function(x) system(paste("gzip -d", x)))
GSM2252974_6181.sst-rma-gene-full.chp.gz 
                                       0 
GSM2252975_6185.sst-rma-gene-full.chp.gz 
                                       0 
GSM2252976_6186.sst-rma-gene-full.chp.gz 
                                       0 
GSM2252977_6171.sst-rma-gene-full.chp.gz 
                                       0 
GSM2252978_6174.sst-rma-gene-full.chp.gz 
                                       0 
GSM2252979_6180.sst-rma-gene-full.chp.gz 
                                       0 
GSM2252980_6196.sst-rma-gene-full.chp.gz 
                                       0 
GSM2252981_6197.sst-rma-gene-full.chp.gz 
                                       0 
GSM2252982_6208.sst-rma-gene-full.chp.gz 
                                       0 
GSM2252983_6225.sst-rma-gene-full.chp.gz 
                                       0 
GSM2252984_6227.sst-rma-gene-full.chp.gz 
                                       0 
GSM2252985_6232.sst-rma-gene-full.chp.gz 
                                       0 
## try reading a couple of them
> z <- readChp("GSM2252975_6185.sst-rma-gene-full.chp")
> z <- readChp("GSM2252974_6181.sst-rma-gene-full.chp")
## now read all of them
> zlst <- lapply(dir(".", "chp$"), readChp)

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

Login before adding your answer.

Traffic: 233 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6