Identifying differentially expressed genes
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MOHAMMAD • 0
@MOHAMMAD-24781
Last seen 13 hours ago

Hello all,

I have transformed, normalized and batch effect corrected RNA-seq count dataset and I want to identify the Differentially expressed genes

I have noticed that many workflows\packages to identifying Differentially expressed genes take RNA-seq count row data as input. what are the convenient workflows\packages to handle my dataset?

if you can share any useful link or file I will be grateful

thank you in advance!

identifyingDifferentiallyexpressedgenes DESeq2 • 123 views
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the row data is available. my problem is how to handle the batch-effect if i have to use row data as input

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I assume you mean raw data, not row data? Please read the manuals of DESeq2 (or any other tool), they clearly instruct on how to model the batch effect by including it into the design. Also, e.g. Batch Effect in DESeq2, how to control, how to remove it, how to address biological question

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@mikelove
Last seen 2 days ago
United States

DESeq2 doesn't offer any functions for analyzing non-count data. So you may look to other packages (but generally many other packages will also want to use information about the precision of the data, which is tossed in this case).

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