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Different results of spearman correlation between TPM and FPKM

This shouldn't be surprising that you see different correlations between gene expression data when expressed in different units. To see why, let's look at how these units are defined. Let's denote the ...
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Can I Incorporate svaseq() into GSEA/GSVA analysis?

Use removeBatchEffects from limma. The input counts should be on log scale, so vst and ...
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beginner RNA-seq Replicate papers

I like Gierlinksi, et al., Bioinformatics, 2015 for this type of problem. I like this paper because the methods are descriptive and clear, they have lots of figures that you can reproduce along the ...
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Normalization of data with RPkM

It's very unlikely that "a RPKM analysis" is the right answer. Assuming you'd like to do differential expression, using tools like DESeq or EdgeR on the count table are likely to be a better ...
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