differential expression analysis
Hello
For differential expression analysis, I want to use RSEM-log2 transformed data. With edgeR and DESeq2 this is not possible because log2 transformation created negative values and these packages cannot deal with negative values. log2 transformation of to normalize data.
How should I do differential expression analysis now? Thanks
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
Handling Negative Values in Log-Transformed a Dataset for Differential Expression Analysis with Li…
written by Maryam •
-
NA Values Appearing After Log Transformation of array Data
written by frankhailey645 •
-
Obtention of the binomial transformed count table with edgeR
written by sofiablancoglez •
-
Manually calculating log2 fold change values from DESeq2 normalized counts
written by jayeshkumarsundaram •
-
A question regarding log2 transformation in EdgeR
written by RNAseqer
-
differential expression analysis with DESeq2 & edgeR
written by Rob •
-
Negative values HTSeq2
written by Rob •
-
RNAseq Variance calculation
written by Rob •
-
How to convert log2FC (Fold Change) obtained by differential expression analysis by DESeq2 to FC
written by sole.r.v •
-
Tcga Mirnaseq Differential Analysis: U-Test Or Edger-Like Approaches On Rpm Values
written by B. Arman Aksoy
Don't you mean: If you sample size is
largeso the whole dispersion estimation etc. becomes less important? What would be the point of a Wilcox/MWU with say n=3 per group, p-values are bound to sample size in case of low n.Hi Kevin Thank you. Do you mean limma and eBayes can work with negative values of log2 transformed dsata?
Hi,
If your goal is differential expression analysis, you can use RSEM expected counts with edgeR and DESeq2.
This is the other logical option, if gene length has been retained (it can be calculated manually, though). You would have to transform the data back to the unlogged scale, too.
Why are you avoiding the standard DESeq2 or edgeR pipelines which use raw counts? Why do you need to log them first yourself?
Hi Swbarnes2 The reason that I do not use raw count is that my supervisor asked me to use standard data that is normal. He did not accept what I did with raw data. He says use RSEM log transformed because that is normal.
I am really confused about what is correct way.
Please show this to your supervisor: https://support.bioconductor.org/p/90672/#90678
Hello rhasanvandj.
Please do not create duplicate posts: RNAseq Variance calculation