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How to analyze LINCS 1000 gz data

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?

lincs r
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written by Md. Al - Mustanjid • Md. Al - Mustanjid

1 answer

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

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written by ArcticPear • ArcticPear

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