I'm trying to convert the file gpl570_family.soft to a csv file in order to load it to excel and getting an error. Can you help me with the syntax? The soft file exists in the working directory (134 GB). I tried many parses but always getting an error message. Thank you, Yossi
>write.csv("GPL570_family.soft", file="GPL570_family.soft.csv")
Error in file(file, ifelse(append, "a", "w")) :
cannot open the connection
In addition: Warning message:
In file(file, ifelse(append, "a", "w")) :
cannot open file 'GPL570_family.soft.csv': Permission denied
#Alternatively:
> write.csv(x,file='gpl570.csv')
> x <- GPL570_family.soft
> file.exists("gpl570.csv")
[1] TRUE
Than I only gets an Excel file named gpl570.csv containing the words x 1 GPL570
#Should I start with read.csv?
Thank you, James. Because data of a platform in GEO is only available in SOFT or MINIMAL formats incontrast to datasets which can be downloaded as CEL files.
I edited my question to be more clear.
The file you can download is a bit, um, difficult to parse, I agree. You can get it from GEOquery:
z <- Table(dataTable(getGEO("GPL570", GSEMatrix = FALSE)))Which will be a data.frame that you can save. But this is just a hard way to get something you can download from Affy directly.
And if you are planning to use these data to annotate something that you are processing using Bioc tools, then you should be using the hgu133plus2.db package.