Hello.
I'm a beginner at Programming with R. now i'm trying to download and parse GEO SOFT format file into an R data structure. when is use the following function:
gset = getGEO(series, GSEMatrix = TRUE, AnnotGPL = TRUE, destdir = "Data/")
using the class(gset)
function , the object stored in the gset
variable is a list, which is the way that I intended to do:
class(ggset)
[1] "list"
But when is try to load the same downloaded data via getgeo()
into the variable gset
, using the following code:
getGEO(filename="Data/GSE9476_series_matrix.txt.gz", GSEMatrix = TRUE, AnnotGPL = TRUE)
the class(gset)
function, returns the following:
class(ggset)
[1] "ExpressionSet"
attr(,"package")
[1] "Biobase"
I can't understand what i'm doing wrong in the second scenario and will be grateful if someone could kindly explain.
Please use the formatting bar (especially the
code
option) to present your post better. You can use backticks for inline code (`text` becomestext
), or select a chunk of text and use the highlighted button to format it as a code block. I've done it for you this time.Thank you, i wasn't familiar with the formating. will do excatly as you did from now on. :)