Problem in getting SNAI1 gene in prostate DEG table

Question

[Maryam]

Hello everyone, would you please help me I have got prostate DEGs by TCGAbiolinks package but I couldn't get SNAI1 gene in my DEG table. I wonder why it does happen. First I normalized it and then I filtered it, even after filtering once, I could not get the gene.

[rpolicastro]

You should include your code, especially the filtering part.

[Maryam]

Yes sure.

#

pradquery <- GDCquery(project = "TCGA-PRAD", data.category = "Transcriptome Profiling", data.type = "Gene Expression Quantification", workflow.type = "STAR - Counts", legacy = F, experimental.strategy = "RNA-Seq")

GDCdownload(query = pradquery, method = "api",)
pradprpr <- GDCprepare(query = pradquery, summarizedExperiment = T)

pradprepro <- TCGAanalyze_Preprocessing(object = pradprpr, cor.cut = 0.6)

bar <- data.frame(colnames(pradprepro))

colnames(bar) <- "barcode"

bar$substr <- substr(bar$barcode, 14,15)

bar <- bar[order(bar$substr, decreasing = T),]

preExpr <- pradprepro[ , as.character(bar$barcode)]

gr <- c(rep("normal", 52), rep("cancer", 501))

gr <- factor(gr)

design <- model.matrix(~ 0 + gr)

colnames(design)<- levels(gr)

pradNorm <- TCGAanalyze_Normalization(tabDF = preExpr, geneInfo = geneInfoHT)

pradFilt <- TCGAanalyze_Filtering(pradNorm, method = "quantile", qnt.cut = 0.25)

library(limma) v <- voom(pradFilt, design = design, plot = T)

E <- v$E

C <- bar[bar$substr < 10,]

N <- bar[bar$substr> 10,]

sampleNT <- TCGAquery_SampleTypes(barcode = N$barcode, typesample = "NT")

sampleTM_TP <- TCGAquery_SampleTypes(barcode = C$barcode, typesample = c("TP","TM"))

ex <- 2^E

ex <- log2(ex+1)

NTdata<- ex[,as.character(sampleNT)]

TMTPdata <- ex[, as.character(sampleTM_TP)]

DEG <- TCGAanalyze_DEA(mat1 = TMTPdata, mat2 = NTdata, Cond1type = "Tumor", Cond2type = "Normal", method = "glmLRT", fdr.cut = 0.05, logFC.cut = 0)