User: evocanres
evocanres • 0
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Posts by evocanres
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Comment:
C: Genes that have NOT changed
... resLA <- results(dds, lfcThreshold=.5, altHypothesis="lessAbs") sum(!is.na(resLA$padj) < 0.1)
can we say, this is the number of genes which are NOT different within logfoldchange of 0.5 ?
...
written 6 months ago by
evocanres • 0
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Comment:
C: Genes that have NOT changed
... Thank you Micheal, I did read it would be incorporated in the package, but didn't read the vignette carefully I guess.
Am I correct in reading that "lessAbs - |β| < x - p values are the maximum of the upper and lower tests " is the replacement for the that code for TOST (test for equivalency)? ...
written 6 months ago by
evocanres • 0
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Comment:
A: Genes that have NOT changed
... I am trying to put the code that was run :) running into formatting issues
...
written 6 months ago by
evocanres • 0
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Comment:
C: Genes that have NOT changed
... 2. If I can replace that with
betaSE <- rowData(dse)$SE_condition_untreated_vs_treated` because
all.equal(mcols(dse), rowData(dse))
gives
>TRUE
> pvalDE <- 2 * pnorm( abs( beta ), sd = betaSE, lower.tail=FALSE )
> all( abs( pvalDE - results(dse)$pvalue ) < 1e-15, na.rm=TRUE ) ...
written 6 months ago by
evocanres • 0
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Comment:
C: Genes that have NOT changed
... I tried to run the exact code ```{r} > # Let's use the example data from the pasilla package > library( DESeq2 ) > library( pasilla ) > data( "pasillaGenes" ) > > # Create a DESeq2 data object from the pasilla data > dse <- DESeqSummarizedExperimentFromMatrix( + counts(pasill ...
written 6 months ago by
evocanres • 0
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... Hi
I am trying to follow through this post as an exercise to find genes that are not differentially expressed. Few things in this post does not work [anymore]. Can somehow help ?
1
Specifically,
1. DESeqSummarizedExperimentFromMatrix. #does not work
#Instead I use the `DESeqDataSetFromMatrix` t ...
written 6 months ago by
evocanres • 0
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Comment:
C: DESeq results gives all genes
... Thank you. That helped actually.
...
written 6 months ago by
evocanres • 0
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... Hi,
I have datasets for 3 different conditions["WT", "KO", "KO1"] (each with 3 replicates). [and two time points["0" and "12"]].
To use in DESeq, I have constructed a DSElist, with design ~ group where group has 6 levels.
dds <- DESeqDataSetFromMatrix(countData = readCount,
...
written 6 months ago by
evocanres • 0
• updated
6 months ago by
Michael Love ♦ 24k
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... Hi,
I would appreciate any suggestions. I have three genotypes and two treatments.
kable(readCountColData)
sampleList |genotype |timePoint |group |
|:----------|:--------|:---------|:------|
|WT_0_1 |WT |0 |WT_0 |
|WT_0_2 |WT |0 |WT_0 |
|WT_0_3 |WT ...
written 6 months ago by
evocanres • 0
• updated
6 months ago by
Michael Love ♦ 24k
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... I figured out. In my samplelist i.e readCountcolData, I should have the group as a column.
...
written 6 months ago by
evocanres • 0
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