Hi, 

I want to practice annotation with this study: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE38376

But I've never worked with GPL files, the type of this file is bgx, I've only practiced with GSM files which were in CEL file type. How do i read these file in R???

Thanks,

Anna

Hi Anna,

You can read BGX files using the package illumiaio.  The following code will take the tar archive you can download from GEO, extract the bgx to a temporary directory and then read it in.

library(illuminaio)
td <- tempdir()
untar("~/Downloads/GSE38376_RAW.tar", exdir = td)
bgx <- readBGX(file.path(td, "GPL6947_HumanHT-12_V3_0_R1_11283641_A.bgx.gz"))

Alternatively, you could also use one of the pre-built annotation packages for the platform, such as this one.

http://bioconductor.org/packages/illuminaHumanv3.db/

Thank you and now Im confused how do I continue , i want to do a quality controll and a gene list of differentialy expressed genes, so then i can do gsea.

First do i have to read the txt file where there are the filename and sample names?

filename  sample
GPL6947_HumanHT-12_V3_0_R1_11283641_A.bgx.gz  SKBR3_Control_1
GPL6947_HumanHT-12_V3_0_R1_11283641_A.bgx.gz     SKBR3_Control_2
GPL6947_HumanHT-12_V3_0_R1_11283641_A.bgx.gz    SKBR3_Control_3
GPL6947_HumanHT-12_V3_0_R1_11283641_A.bgx.gz    SKBR3_0.1uM_Lapatinib_1
GPL6947_HumanHT-12_V3_0_R1_11283641_A.bgx.gz    SKBR3_0.1uM_Lapatinib_2
GPL6947_HumanHT-12_V3_0_R1_11283641_A.bgx.gz    SKBR3_0.1uM_Lapatinib_3
GPL6947_HumanHT-12_V3_0_R1_11283641_A.bgx.gz    SKBR3_1uM_Lapatinib_1
GPL6947_HumanHT-12_V3_0_R1_11283641_A.bgx.gz     SKBR3_1uM_Lapatinib_2
GPL6947_HumanHT-12_V3_0_R1_11283641_A.bgx.gz     SKBR3_1uM_Lapatinib_3
GPL6947_HumanHT-12_V3_0_R1_11283641_A.bgx.gz     SKBR3-R_Control_1
GPL6947_HumanHT-12_V3_0_R1_11283641_A.bgx.gz     SKBR3-R_Control_2
GPL6947_HumanHT-12_V3_0_R1_11283641_A.bgx.gz     SKBR3-R_Control_3
GPL6947_HumanHT-12_V3_0_R1_11283641_A.bgx.gz     SKBR3-R_0.1uM_Lapatinib_1
GPL6947_HumanHT-12_V3_0_R1_11283641_A.bgx.gz     SKBR3-R_0.1uM_Lapatinib_2
GPL6947_HumanHT-12_V3_0_R1_11283641_A.bgx.gz     SKBR3-R_0.1uM_Lapatinib_3
GPL6947_HumanHT-12_V3_0_R1_11283641_A.bgx.gz     SKBR3-R_1uM_Lapatinib_1
GPL6947_HumanHT-12_V3_0_R1_11283641_A.bgx.gz     SKBR3-R_1uM_Lapatinib_2
GPL6947_HumanHT-12_V3_0_R1_11283641_A.bgx.gz     SKBR3-R_1uM_Lapatinib_3

# create sampleNames from the list of txtFile - substitute file names with sample names
txtFiles <- list.files()
txtFiles <- txtFiles[txtFiles!="filename2sample.txt"]
fn2sp <- read.table(filename2sample, header=T, sep='\t')

At this point it says that "Error in scan(file, what, nmax, sep, dec, quote, skip, nlines, na.strings,  : 
  line 1 did not have 2 elements"  why??

Then I do an rma and exprs,boxplot etc and then with limma and with illuminaHumanv3.db i can have the differencialy expressed gene list, no?