In this case you have to prepare the
gct file "by hand" for analyze your data with GSEA. Once you have created your DESeq object (
dds) you are going to retrieve the normalized counts based on the DESeq method:
norm_counts <- counts(dds, normalized = T)
Then, you must arrange this normalized counts matrix according to the minimum requirements for a GCT file.
I suggest you to codificate the
norm_counts as a
data.frame and add an extra column called description (this column could contain the id's of your genes):
norm_counts <- as.data.frame(norm_counts)
norm_counts$description <- norm_counts$your_id_column
Move the "description" column to be the second in the df and save it using the
write.table(norm_counts, "path_to_save_file.gct", sep = "\t", quote = F, row.names = F)
Finally, using a plain text editor put all the additional information (following the directions of the link) to have a gct file for GSEA.
For a detailed tutorial about
cls files watch this video but please follow the directions of the link
Hope it could help!