hi @Jiahui
it seems you have only two samples, while the latest versions of edgeR require replicates, hence “Only 2 columns of data: need at least 3”. The best option is to have replicates, at least for one condition. Alternatives: old versions might support analysis without replicates. Try an earlier versions of DESeq2 and/or edgeR. Cuffdiff supports analysis without replicates, at least old versions did.
Hope this helps.
Kind regards,
Igor
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