Dear all I am analyzing my data of GEO using R and got the below error. Please guide me in this regards, Raheleh
tasks <- c("sorted.download_data")
source("runall.R")
Found 1 file(s)
GSE20853_series_matrix.txt.gz
Using locally cached version: ~/proj/lung/data/Kyoto_Expression/GSE20853_series_matrix.txt.gz
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
|=================================================================| 100% 70 MB
Using locally cached version of GPL962 found here:
~/proj/lung/data/Kyoto_Expression/GPL962.annot.gz
Error in df$fudan <- NA : object of type 'closure' is not subsettable
> tasks
[1] "sorted.download_data"
1 answer
gset <- getGEO("GSE20853", GSEMatrix =TRUE, destdir = "~/proj/lung/data/Kyoto_Expression", AnnotGPL=TRUE)[[1]] Found 1 file(s) GSE20853_series_matrix.txt.gz Using locally cached version: ~/proj/lung/data/Kyoto_Expression/GSE20853_series_matrix.txt.gz Parsed with column specification: cols( .default = col_double() ) See spec(...) for full column specifications. |=================================================================| 100% 70 MB Using locally cached version of GPL962 found here: ~/proj/lung/data/Kyoto_Expression/GPL962.annot.gz
fvarLabels(gset) <- make.names(fvarLabels(gset)) gsms <- paste0 sml <- c() for (i in 1:nchar(gsms)) { sml[i] <- substr(gsms,i,i) } Error in nchar(gsms) : cannot coerce type 'closure' to vector of type 'character'
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just check if file
GSE20853_series_matrix.txt.gzis unzipped and a data frame is created within R, before trouble shooting. Also check if script accommodates gz files or not.I unzipped the file and ran again, but the error exits yet,
In general, this happens when you index some thing that is not sub-settable (for eg. a function). Without code and example it may not be easy to troubleshoot the issue. Look at this object
sorted.download_datawould you please guide me for creating a data frame.
I am not sure about the contents of
runall.Randsorted.download_data. Without that it is not possible to understand the error (for me). Keep printing thetypeof the objects you have in the current workspace.I need more documents for studying.
I would appreciate to provide more details for me in this matter.
This is not how this community works. Please be patient. We are driven by volunteers and not on-demand supporters. Your question is only 5h old by now (which is not much and it is a Saturday) and your post lacks details which currently prevents us from providing help.
=> As cpad0112 mentioned already, please show the content of that script you are running. Without that it is impossible to help.
The comment was:
The code is here;
for (i in 1:nchar(gsms)) { sml[i] <- substr(gsms,i,i) } Error in nchar(gsms) : cannot coerce type 'closure' to vector of type 'character'
I doubt that is the full code. Where is
df$fudan <- NAfrom the toplevel question and where does gsms and sml even comde from? If you want people to provide help please show full code.