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Old 02-24-2019, 11:15 AM   #1
Location: Italy

Join Date: Jul 2017
Posts: 34
Default RNAseq without technical replicates

Dear all,

I want to download RNAseq files of tumor cell lines from GEO and compare between them.
I know that I can not use DESeq2 if I don't have technical replicate, so I want to ask what is the best way to analyses DE profiling between samples without replicate?

what package best fit instead of DESeq2 ?

thank you

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Old 02-24-2019, 03:43 PM   #2
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You are confusing technical replicates with biological ones. What you want is biological replicates (which some GEO data may have). People rarely do technical replicates now a days.
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Old 02-24-2019, 09:09 PM   #3
Location: Italy

Join Date: Jul 2017
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Hi GenoMax,

What I want to do is to compare the expression profile of cell lines of the same type of tumor. They do not have technical replicates ,they are named CUTLL1, KOPTK1, PF382, DND41.

What would you do ?

Thank you

Last edited by NDUFB11; 02-24-2019 at 09:13 PM.
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