How to analyze LINCS 1000 gz data

Question

[Md. Al - Mustanjid]

I need to analyze a LINCS dataset for my research study. I have downloaded the level-5 LINCS data from the NCBI Geo database (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE70138) in gctx.gz format. I have tried typically data.table library in R to read the file but got an error; further, I extracted the gct file from gz file, then I also used the cmapR package to analyze data but got gct parse file error.

Is there any way to get level-5 LINCS data in CSV format? or how can I analyze level-5 LINCS data?

Answer 1

[ArcticPear]

I just joined this site so sorry for the late reply. If you still haven't figured it out the answer could be here: https://www.rdocumentation.org/packages/CePa/versions/0.8.0/topics/read.gct

[Md. Al - Mustanjid]

Thanks for helping, sorry to say that the link is not working.