User: Matan G.

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Matan G.0
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Posts by Matan G.

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Comment: C: Batch correction in DESeq2
... Thank you. By saying "This is just normalization for sequencing depth" you mean when using the following DESeq function: DESeq2 using: dds <- estimateSizeFactors(dds); counts(dds, normalized=TRUE) ? So the other normalization (ie vst(dds)) takes other things into consideration? Best ...
written 3 days ago by Matan G.0
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Comment: C: Batch correction in DESeq2
... Hi Michael, There is a great difference between the normalized count table when using: vsd <- vst(dds) assay(vsd) WITHOUT batch removal compared to the normalized count table generated by DESeq2 using: dds <- estimateSizeFactors(dds); counts(dds, normalized=TRUE) In order to compare the tw ...
written 3 days ago by Matan G.0
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Normalized counts access in DESeq2 R: with and without batch
... As described previously here: https://support.bioconductor.org/p/66067/ The way to access the normalized count table in DESeq2 can be done by the following script lines: dds <- estimateSizeFactors(dds) counts(dds, normalized=TRUE) I'm trying to understand if the normalized count table that can ...
normalization edger deseq2 written 7 days ago by Matan G.0 • updated 7 days ago by Michael Love26k
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Comment: C: DESeq2 using 'relevel' for different comparisons
... Thank you for the prompt reply. I have read the contrast argument section. 1. If you use the contrast argument you discard the relevel (ie deactivate it)? 2. In one of the vignettes, it written that there is a great importance for writing the control/reference first. How does the contrast argum ...
written 10 days ago by Matan G.0
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DESeq2 using 'relevel' for different comparisons
... Let's say that I have RNA seq data with multiple clinical conditions from multiple patients/samples. As far as I understand, the first level that is used is the reference level that other conditions will be compared to. For example if I have the following conditions: 1. Control 2. Treatment 1 3. Tre ...
deseq2 written 10 days ago by Matan G.0 • updated 10 days ago by Michael Love26k

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