Question: Error in ncol(eset) 'eset.filt' not found
0
gravatar for cpyadav22
6 months ago by
cpyadav220
cpyadav220 wrote:

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 • 156 views
ADD COMMENTlink modified 6 months ago by James W. MacDonald51k • written 6 months ago by cpyadav220
Answer: Error in ncol(eset) 'eset.filt' not found
0
gravatar for James W. MacDonald
6 months ago by
United States
James W. MacDonald51k wrote:

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 COMMENTlink written 6 months ago by James W. MacDonald51k

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 REPLYlink written 6 months ago by cpyadav220

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 REPLYlink written 6 months ago by James W. MacDonald51k

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

ADD REPLYlink written 6 months ago by cpyadav220

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 REPLYlink modified 6 months ago • written 6 months ago by Martin Morgan ♦♦ 23k

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 REPLYlink written 6 months ago by cpyadav220
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 237 users visited in the last hour