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Comment: Error for AnnotationForge makeOrgPackageFromNCBI function
by
James W. MacDonald
67k
That error indicates that you have a file called NCBI.sqlite in your working directory that is missing some tables. You should delete that …
Comment: Are transformed values from rlog /vst log2 normalized counts?
by
James W. MacDonald
67k
The `DESeq2` package is meant to analyze count data! Most packages that are intended to be used for RNA-Seq data are going to want the raw …
Comment: Are transformed values from rlog /vst log2 normalized counts?
by
Eva
▴ 10
Many thanks for you detailed answer, I really appreciate it. Could you give me an example (or more if possible) of analysis using count-b…
Comment: Error for AnnotationForge makeOrgPackageFromNCBI function
by
Gabriela
• 0
Hi, I have the same issue as you! Does this happen because of internet speed? I already downloaded 2 times these files! > makeOrgPacka…
Answer: Are transformed values from rlog /vst log2 normalized counts?
by
James W. MacDonald
67k
They are not counts because counts are integers. ``` > z <- makeExampleDESeqDataSet() ## These are counts > head(assay(z)) sam…
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Answer: Unable to install any Bioconductor package with new R 4.4.1 - path nor writable
Removing Effect of Covariate in Only a Subset of Samples in a Model Containing All Samples Loses Full Rank if Factor but not Numerical
Comment: How to conduct maSigPro analysis with only one condition?
Comment: How to conduct maSigPro analysis with only one condition?
Comment: Spectra and PSMatch- trouble in reducePSMs, joinSpectraData, or countIdentificat
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