Question

project miran packages

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cpyadav22 • 0

@cpyadav22-20185

Last seen 5.6 years ago

MiRNA cel file is not being read in Bioconductor R. R version is 3.5.2 Rstudio massage is following: "Couldn't obtain CDF environment, problems encountered: specified environment does not contain miRNA-3_0 Library -package mirna30cdf not installed Bioconductor - mirna30cdf not available"

If anybody can help, please do it

mirna30cdf packages • 913 views

ADD COMMENT • link updated 5.7 years ago by Guido Hooiveld ★ 4.1k • written 5.7 years ago by cpyadav22 • 0

score 0 · Answer 1 · 2019-03-13

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Guido Hooiveld ★ 4.1k

@guido-hooiveld-2020

Last seen 1 day ago

Wageningen University, Wageningen, the …

Affymetrix (and hence Bioconductor) doesn't provide a chip definition file (CDF) for this type of array. To process your CEL files you will need the oligo package (here) and corresponding platform design package (here). You may want to check e.g. this post of James McDonald (here) for some code to get you started. [Obviously you have to modify the name of the PdInfo package as well as the location of your CEL files...]

ADD COMMENT • link 5.7 years ago Guido Hooiveld ★ 4.1k

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i have excused following command given your link but any solution come out.

setwd("C:/Users/Chandan Yadav/Desktop/New folder/chandan") library(pd.mirna.3.0) library(oligo) library(pd.mirna.3.0) celFiles <- list.celfiles("~/Desktop/AffymetrixmiRNA/RawDatamiRNA", full.names=TRUE) rawData <- read.celfiles(celFiles, pkgname="pd.mirna.3.0") All the CEL files must be of the same type. Error in read.celfiles(celFiles, pkgname = "pd.mirna.3.0") : checkChipTypes(filenames, verbose, "affymetrix", TRUE) is not TRUE

ADD REPLY • link 5.7 years ago cpyadav22 • 0

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The error you got:

 All the CEL files must be of the same type.

is rather self-explanatory. It means that either a) you have an experiment consisting of some CEL files that you think are mirna 3.0 arrays, but rather are (all) of a different type; or b) that your CEL files are of 'mixed origin' [you thus have e.g. some 3.0 arrays, but also 4.0 arrays].

Easiest to do is NOT to specify the PdInfo package when reading-in the CELL files (situation a). Thus do:

rawData <- read.celfiles(celFiles) #pkgname argument is not specified

If this doesn't work either, then likely situation b) is at hand. I would then suggest to read ech CEL file separately/individually to check which ones are different.

ADD REPLY • link 5.7 years ago Guido Hooiveld ★ 4.1k