Hi All,
I ran my RNAseq Illumina Hiseq 50x50 data through DESeq, no replicates, and as a first step obtained my annotations via -
txdb <- makeTranscriptDbFromUCSC(genome = "hg19", tablename = "refGene")
exonRangesList <- exonsBy(txdb, "gene")
After DESeq I have results such as -
id baseMean baseMeanA baseMeanB foldChange log2FoldChange pval
22410 653048 1820.9684 0 3641.9369 Inf Inf 2.183608e-96
22411 653067 1820.9684 0 3641.9369 Inf Inf 2.183608e-96
22412 653219 1820.9684 0 3641.9369 Inf Inf 2.183608e-96
22413 653220 1820.9684 0 3641.9369 Inf Inf 2.183608e-96
22638 9503 1820.9684 0 3641.9369 Inf Inf 2.183608e-96
14024 7345 318.4127 0 636.8254 Inf Inf 8.684167e-23
I would appreciate it if someone would explain to me (a newbie) -
1. what exactly my "id" refers to in the output - ie. transcripts/exons/refgenes?
2. how to obtain corresponding refgene for the output so I can look to see if there are changes in genes of interest
Thanks a lot!
I ran my RNAseq Illumina Hiseq 50x50 data through DESeq, no replicates, and as a first step obtained my annotations via -
txdb <- makeTranscriptDbFromUCSC(genome = "hg19", tablename = "refGene")
exonRangesList <- exonsBy(txdb, "gene")
After DESeq I have results such as -
id baseMean baseMeanA baseMeanB foldChange log2FoldChange pval
22410 653048 1820.9684 0 3641.9369 Inf Inf 2.183608e-96
22411 653067 1820.9684 0 3641.9369 Inf Inf 2.183608e-96
22412 653219 1820.9684 0 3641.9369 Inf Inf 2.183608e-96
22413 653220 1820.9684 0 3641.9369 Inf Inf 2.183608e-96
22638 9503 1820.9684 0 3641.9369 Inf Inf 2.183608e-96
14024 7345 318.4127 0 636.8254 Inf Inf 8.684167e-23
I would appreciate it if someone would explain to me (a newbie) -
1. what exactly my "id" refers to in the output - ie. transcripts/exons/refgenes?
2. how to obtain corresponding refgene for the output so I can look to see if there are changes in genes of interest
Thanks a lot!
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