co expression network

Question

[gbahramali]

Hello I WANT TO USE coexnet PACKAGE OF BIO CONDUCTOR BUT AFTER DOWNLOADED GSE AND GPL.SOFT I SEE THIS ERROR

getInfo(GSE = "GSE34228", GPL = "GPL4133",directory = ".") trying URL 'https://ftp.ncbi.nlm.nih.gov/geo/series/GSE34nnn/GSE34228/suppl//GSE34228_RAW.tar?tool=geoquery' Content type 'application/x-tar' length 482160640 bytes (459.8 MB) downloaded 459.8 MB

File stored at: ./GPL4133.soft

gene_table <- geneSymbol(GPL = "GPL4133",directory = system.file("extdata",package = "coexnet")) Error in data.frame(sym$ID, gsub(" /// ", "-", sym$GENE SYMBOL), stringsAsFactors = FALSE) : arguments imply differing number of rows: 45220, 0 HOW CAN DEAL WITH THIS ERROR

Answer 1

[pbpanigrahi]

Hi

Can you try the code below and post the output

gpl <- "./GPL4133.soft"  
sym <- Table(gpl)
print(str(sym));

Also check column names in soft file

From the geneSymbol function of coexnet package

sym <- Table(gpl)

ta <- data.frame(sym$ID, gsub(" /// ","-",sym$GENE SYMBOL), stringsAsFactors = FALSE)

It seems it could find sym$ID (total 45220) but not sym$GENE SYMBOL (0 rows). Thats why it is not able to create a data frame.

Check whether in GPL4133.soft file whether GENE SYMBOL is there or not? If something else is there, then you need to modify GENE SYMBOL with the particular column name.

We need more input info from you to pinpoint the result

[gbahramali]

thanks for your reply try it but show error

gpl <- "./GPL4133.soft"
sym <- Table(gpl) Error in Table(gpl) : could not find function "Table" print(str(sym)); Error in str(sym) : object 'sym' not found

[pbpanigrahi]

Hi

Maybe Table is an internal function. I tried to search for it coexnet package, couldn't get.

Anyhow if you go the link, you can see in the table, its GENE_SYMBOL and not GENE SYMBOL.

The geneSymbol function code has `GENE SYMBOL`. To fix this, you manually edit the geneSymbol function and run. Here i am showing below

#Load the library and Overwrite the function
library(coexnet);
geneSymbol <- function(GPL, directory = "."){
  options(warn=-1)
 gpl <- getGEO(filename = paste0(directory,"/",GPL,".soft"))
 sym <- Table(gpl)
 names(sym) <- toupper(names(sym))
 ta <- data.frame(sym$ID, gsub(" /// ","-",sym$`GENE_SYMBOL`), stringsAsFactors = FALSE)
 names(ta) <- c("probe","ID")
  return(ta)
}

Then call the function.

I have replaced sym$`GENE SYMBOL` to sym$`GENE_SYMBOL`. If this does not work try replacing with sym$GENE_SYMBOL (Remove the two quotes)

Hope this solves.

[gbahramali]

HI thanks for your reply i used gpl8715 this gpl didnot have genesymbol and have description how can deal with this problem thanks again

[pbpanigrahi]

Did u try what I have suggested.