lncRNA Differential Expression Analysis
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sushimoto • 0
@2fc02fda
Last seen 11 weeks ago
Turkey

I have a very straightforward question. Please accept my apologies, I am very new to RNASeq data analysis. Can I do a limma or DESeq2 analysis of the data obtained from these two datasets:

1) LGG lncRNA data from TANRIC database (https://ibl.mdanderson.org/tanric/_design/basic/download.html)

2) Healthy brain samples from Xena (https://xenabrowser.net/datapages/?dataset=TCGA-GTEx-TARGET-gene-exp-counts.deseq2-normalized.log2&host=https%3A%2F%2Ftoil.xenahubs.net&removeHub=https%3A%2F%2Fxena.treehouse.gi.ucsc.edu%3A443). Dataset: gene expression RNAseq - RSEM expected_count (DESeq2 standardized).

I am trying to detect differentially expressed lncRNA between healthy brain samples and LGG samples.

Thank you in advance.

DESeq2 limma RNASeqData • 252 views
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@mikelove
Last seen 11 hours ago
United States

I don't think this is a good idea, because the two groups have two variables perfectly confounded: site + condition. So you can't tell what is a site difference and what is a condition difference.

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Thank you for your response Michael.

The sites are the same in both datasets, which would be the brain. The condition is different, which is desired. Please correct me if I am wrong.

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I mean site as in the location of the experiment. This induces large differences which cannot be controlled in the case of perfect confounding (as in this example).

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