search

zwdzwd / sesame

🍪 SEnsible Step-wise Analysis of DNA MEthylation BeadChips
Other
58 stars 31 forks source link

How to solve problem with error : $ operator is invalid for atomic vectors? #158

Open TPlatek opened 6 months ago

TPlatek commented 6 months ago

Hello, I am trying to analyse my methylation DNA EPIC v 2.0 arrays with sesame. I am using windows and really new to R and Sesame.

After the code: readIDATpair("208133980083_R01C01","manifest=mft") There is an error: Error in mft$col : $ operator is invalid for atomic vectors.

Could everyone please advise me how to solve this problem?

list.files(pattern = "*.idat") library(sesame) s=readIDATpair("208133980083_R01C01") s mft <- read.csv("C:/Wyniki_EPIC_GenomeScan/Dane/R/EPICv2.0manifest/EPIC-8v2-0_A1.csv", header = T, stringsAsFactors = F, na.strings = c("NA", "")) setwd("C:/Wyniki_EPIC_GenomeScan/Dane/R") mft <- read.csv("C:/Wyniki_EPIC_GenomeScan/Dane/R/EPICv2.0manifest/EPIC-8v2-0_A1.csv", header = T, stringsAsFactors = F, na.strings = c("NA", "")) head(mft) readIDATpair("208133980083_R01C01","manifest=mft")

Error in mft$col : $ operator is invalid for atomic vectors

zwdzwd commented 6 months ago

Hi, what's your version number with sesame_checkVersion()? sounds like it's a version issue.

TPlatek commented 6 months ago

Hi, Here are my packages versions:

sesame_checkVersion() SeSAMe requires matched versions of R, sesame, sesameData and ExperimentHub. Here is the current versions installed: R: 4.3.3 Bioconductor: 3.18 sesame: 1.20.0 sesameData: 1.20.0 ExperimentHub: 2.10.0

Kind regards, Teresa Płatek

W dniu 2024-04-15 13:17, Wanding Zhou - Bioinformatics napisał(a):

Hi, what's your version number with sesame_checkVersion()? sounds like it's a version issue.

-- Reply to this email directly, view it on GitHub [1], or unsubscribe [2]. You are receiving this because you authored the thread.Message ID: @.***>

Links:

[1] https://github.com/zwdzwd/sesame/issues/158#issuecomment-2056581421 [2] https://github.com/notifications/unsubscribe-auth/BH2UCOEPTE3KOPWVAAUFVL3Y5OZMNAVCNFSM6AAAAABGG4OZM2VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDANJWGU4DCNBSGE

zwdzwd commented 6 months ago

for this version, I don't think you need mft argument. EPICv2 is supported by default. Have you tried just readIDATpair("208133980083_R01C01")