Question

Pathway analysis and GO terms analysis with goseq

0

Entering edit mode

ojong • 0

@ojong-24301

Last seen 23 months ago

United States

ddsMat <- DESeqDataSetFromMatrix(countData = fcts,colData = sampleinfo,design = ~ Treatment)

dds <- DESeq(ddsMat,betaPrior=TRUE)

res <- results(dds) # Extract results
library(goseq)
genes=as.integer(p.adjust(res$pvalue[res$log2FoldChange!=0],
method="BH")<.05)
names(genes)=row.names(res[res$log2FoldChange!=0,])
table(genes)


library(TxDb.Hsapiens.UCSC.hg38.knownGene)
TxDb= TxDb.Hsapiens.UCSC.hg38.knownGene

head(supportedOrganisms())
supportedOrganisms()[supportedOrganisms()$Genome=="hg38",]

pwf=nullp(genes,"hg38","ensGene")
head(pwf)

Error message for GO terms analysis with goseq

KEGG Pathways GO goseq • 1.4k views

ADD COMMENT • link updated 4.0 years ago by James W. MacDonald 67k • written 4.0 years ago by ojong • 0

0

Entering edit mode

Please, I am stuck with this task. I am trying to perform Gene ontology and KEGG pathway analysis with goseq package. The error message says the gene names specified do not match the gene names for genome hg38 and ID ensGene. I would be glad with any help in achieving this analysis. Thanks in advance

ADD REPLY • link 4.0 years ago ojong • 0

score 2 · Answer 1 · 2020-12-07

The error message you received is intended to be self-explanatory, so let's recap. The error says, if I restate (since you included a png to show the output instead of copying and pasting, as requested in the FAQ), 'you gave me a bunch of gene IDs that look like this: ENSG00000227232.5, and yet what I expected looked like this: ENSG00000227232'

And if you look closely at the example IDs, the only difference is a subscript that is a period, followed by a number. Which indicates to me that the answer is to strip off the offending subscript that is being complained about? If you are confused as to how one does that, see ?gsub.