Question

Error in ncol(eset) 'eset.filt' not found

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cpyadav22 • 0

@cpyadav22-20185

Last seen 5.7 years ago

I have downloaded data from EMBL-EBI (ArrayExpression myocardial infarction) Acession number E-MTAB-3573 raw data, cel file name (Wangyaping normal and disease condition, organism HOMO Sapiens). I have used this paper (Microarray Data Analysis for Transcriptome Profiling) command line RUN in Rstudio, Some result has come out such as Data Preprocession, Normalisation Gene Expression, Gene Annotation, quality Assessement, after that Genefilter command line has to RUN the result come out Error in ncol(eset) 'eset.filt' not found. I have atteched this paper PDF. Please sort out this problem. Thanks Dear enter image description here

oligo package • 1.2k views

ADD COMMENT • link updated 5.7 years ago by James W. MacDonald 67k • written 5.7 years ago by cpyadav22 • 0

score 0 · Answer 1 · 2019-04-05

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James W. MacDonald 67k

@james-w-macdonald-5106

Last seen 4 days ago

United States

If you get an error from R saying

Error in ncol(eset) 'eset.filt' not found.

You can interpret that as R saying that this thing you are calling 'eset.filt' doesn't exist. And the reason it doesn't exist is most likely because you never made it (or you tried to, but R gave you another error at that step, saying it couldn't make it).

ADD COMMENT • link 5.7 years ago James W. MacDonald 67k

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I do next step for Gene filter process, first upon install.packages("genefilter"), result has come out Error: unexpected input in " install.packages(" " . external packages install to Biocounductor R, next command line run (eset.filt = varFilter(eset.filt, var.func=IQR, var.cutoff = 0.25, filterByQuantile = TRUE). The result has come out Error in ncol(eset) 'eset.filt' not found.

ADD REPLY • link 5.7 years ago cpyadav22 • 0

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You don't install Bioconductor packages using install.packages.

And my response remains the same. If R gives you that error, it's because the object you are calling 'eset.filter' doesn't exist. Telling us snippets of what you have done isn't helpful - you need to figure out for yourself why that object doesn't exist, and then backtrack to where ever you were supposed to create it and figure out what went wrong.

ADD REPLY • link 5.7 years ago James W. MacDonald 67k

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I have working R version 3.5.3, The genefilter packages is not available in this version. please help me. Thank You Dear

ADD REPLY • link 5.7 years ago cpyadav22 • 0

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Your statement that genefilter is not available for R-3.5.3 is not correct. Have you tried to install it using the instructions on the package landing page?

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("genefilter", version = "3.8")

ADD REPLY • link 5.7 years ago Martin Morgan 25k

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I have not uesd above command' eset.filt', only use command eset. the message come out 'Error in ncol(eSet) : object eSet.filter' not found. Please show this problem. Thank You

ADD REPLY • link 5.7 years ago cpyadav22 • 0