count tables from RNA-seq data on GEOmetadb

Question

[rahel14350]

Dear Sean Davis, I would like to work on the count tables of normal and metastatic samples of Colon (Colorectal) cancer using RNA-seq. I tried this code from GEOmetadb but I did not get all the information. Do you think is there anyway I can address all the data that I want like metastatic or Normal or RNA-seq? Or do you think I should get the fastq files from SRAdb and then start from raw data? Many thanks in advance, Rahel Here is the codes I tried so far:

  sql <- paste("SELECT DISTINCT gse.title,gse.gse",
             "FROM",
             "  gsm JOIN gse_gsm ON gsm.gsm=gse_gsm.gsm",
             "  JOIN gse ON gse_gsm.gse=gse.gse",
             "  JOIN gse_gpl ON gse_gpl.gse=gse.gse",
             "  JOIN gpl ON gse_gpl.gpl=gpl.gpl",
             "WHERE",
             "  gsm.molecule_ch1 like '%RNA%' AND",
             "  gse.title LIKE '%colon cancer%' OR",
             "  gse.title LIKE '%colorectal cancer%' AND",
         " gse.title LIKE '%metastatic%' AND",
             "  gpl.organism LIKE '%Homo sapiens%' ",sep=" ")
rs <- dbGetQuery(con,sql)
dim(rs)

Answer 1

[Sean Davis]

GEOmetadb contains only the "metadata", not the actual RNA-seq counts. You can use GEOquery to access the actual data, if they have been submitted, or you can download fastq from SRA if you have access to the studies (since it appears you are working in human, these files will be protected).

[rahel14350]

Dear Sean, Many thanks for your prompt reply. I did also tried GEOquery but I need to do it per study (GSE*) and then I can use Limma. I can not get the table counts for all of the studies using getGEO(). I also can combine/merge two eset but when they are on the same platform or the number of samples are the same but not when there is differences!. Do you know any other way that I can get all the table counts and use Limma afterwards? Many thanks, Rahel