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MOHAMMAD
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@MOHAMMAD-24781
Last seen 3.6 years 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!
A: Differential expression analysis starting from TPM data
A: RNASeq DE analysis starts from different DESeq2 normalized data, TMM normalized
These two links are probably what you want given the circumstances.
the row data is available. my problem is how to handle the batch-effect if i have to use row data as input
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