Question: Analysing CGH data from GEO Dataset
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gravatar for salvatore.raieli2
23 months ago by
salvatore.raieli260 wrote:

Hi everyone,

I took this dataset from GEO Dataset, CGH data from 129 neuroblastoma patients using this platform: Agilent-014698 Human Genome CGH Microarray 105A (G4412A)

#I used these two libraries
library("GEOquery")
library("limma")

#then I downloaded the file:
GSE45478 <- getGEO('GSE45478', GSEMatrix=TRUE)
gse <- GSE45478$GSE45478_series_matrix.txt.gz    

#I load the expression set, and annotate it:
y <- log2(exprs(gse))
a <- fData(gse)[7]
rownames(y) <- a

#then I used this function for replace replicate probes with their average.
data_set<- as.data.frame(avereps(y, ID = a))

these are the first rows I obtained:

example <- data.frame(
  GeneSymbol = c("ATF2", "LRP1B", "GATS", "RANGAP1", "IL1RAPL1", "FNBP1L", "ZBTB20", "ROBO2", "RERG", "FGF13"), 
  GSM1105244 = c(-4.176808184, -6.29424113, -3.339853967, NA, -3.245990902, -7.658497188, -4.189092613, -3.711020582, -4.880287693, -2.948311002),
  GSM1105245 = c(-5.161793109, -4.909742069, -6.185811131, -11.32774128, -6.311290372, NA, -4.351089627, -4.363281656, -7.764292069, -5.681309704),
  GSM1105246 = c(-4.291192299, -4.858417793, NA, -9.773096718, -2.523649181, -4.089280593, -5.18011826, -4.133100609, NA, -2.47126024),
  GSM1105247 = c(-3.347528128, -4.044713691, -6.050732251, -3.123978152, -1.839342341, -3.516601202, -4.55673305, -2.495130853, NA, -1.865756679)
)

In our lab we have a list of gene, we want to do a preliminary analysis in literature data to know if these genes are deleted in tumors. How I should procede know? how I set a cut-off to consider a gene deleted? I have to some other steps?

Thank you for your helps

cgh limma geoquery R • 599 views
ADD COMMENTlink modified 22 months ago by zx87549.0k • written 23 months ago by salvatore.raieli260
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