Question

DESeq2 setting significant p-value

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Merlin ▴ 10

@merlin-15723

Last seen 4.9 years ago

Vancouver

Hello everyone, I have a question about the p-value that comes out from DESeq2.

Here is the command line that I use:

res <- results(dds, alpha = 0.05)
resultsNames(dds)
resLFC <- lfcShrink(dds, coef=2, res=res, type="apeglm")
resFile <-na.omit(resLFC)
resFile <-resFile[order(resFile$padj),]
write.csv(as.data.frame(resFile),file="~/RNAseq/salmon_folder/file.csv", quote=F)

The p-value and padj have lots of values greated then 0.05 and I’m not sure if I have to remove this values before plotting this data like when I do an heatmap for example.

Thank you

DESeq2 • 1.2k views

ADD COMMENT • link updated 8 months ago by Michael Love 43k • written 5.6 years ago by Merlin ▴ 10

score 2 · Accepted Answer · 2019-05-07

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Michael Love 43k

@mikelove

Last seen 2 days ago

United States

This is totally up to you, but in the workflow we simply plot the top genes by variance. Others will subset to the genes in the FDR set.

ADD COMMENT • link 5.6 years ago Michael Love 43k

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after running DESeq2 does it sort the value on the basis of pvalue, or anything, or does it give the data back in the input format

I have passed an input in DESeq2 where my data has sorted gene names by A-Z, now in results it is not showing the gene names in result. now I want to know if it DESeq2 is sorting the result or not on the basis of pvalue or anything, or i just can use my previous expression file's list and then manually take out the DEGs.

ADD REPLY • link 8 months ago Dev • 0

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It does not resort. Also the dataset and results will have the same row names from object creation throughout the analysis.

ADD REPLY • link 8 months ago Michael Love 43k

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Sir but when I put in the expression data via the csv file, it was showing the gene names then but now when i set it in the form factor it is not showing the result.

ADD REPLY • link 8 months ago Dev • 0

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> counts <- matrix(1:16, ncol=4, dimnames=list(letters[1:4],NULL))
> coldata <- data.frame(x=1:4)
> DESeqDataSetFromMatrix(counts, coldata, ~1)
class: DESeqDataSet
dim: 4 4
metadata(1): version
assays(1): counts
rownames(4): a b c d
rowData names(0):
colnames: NULL
colData names(1): x

Here the rownames are present in the dataset and will be propagated to results.

ADD REPLY • link 8 months ago Michael Love 43k