Hello,

I tried to download a gene expression dataset from GEO site. My code worked perfectly in the past but now suddenly I am receiving error messages. I double-checked the GEO Analyze with GEO2R R script and it looks exactly  just like mine. I tried it on both PC and Mac. No luck.

Any suggestions are highly appreciated.

Anita

My code:

library(Biobase)
library(GEOquery)

gset <- getGEO("GSE8401", GSEMatrix =TRUE)
if (length(gset) > 1) idx <- grep("GPL96", attr(gset, "names")) else idx <- 1
gset <- gset[[idx]]
gset

Error:

> gset <- getGEO("GSE8401", GSEMatrix =TRUE)
ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE8nnn/GSE8401/matrix/
Found 1 file(s)
GSE8401_series_matrix.txt.gz
Using locally cached version: C:\Users\ANITAL~1\AppData\Local\Temp\RtmpMrh4oX/GSE8401_series_matrix.txt.gz
Using locally cached version of GPL96 found here:
C:\Users\ANITAL~1\AppData\Local\Temp\RtmpMrh4oX/GPL96.soft 
Error in xj[i] : only 0's may be mixed with negative subscripts
In addition: Warning message:
closing unused connection 3 (C:\Users\ANITAL~1\AppData\Local\Temp\RtmpMrh4oX/GPL96.soft) 
> if (length(gset) > 1) idx <- grep("GPL96", attr(gset, "names")) else idx <- 1
Error: object 'gset' not found
> gset <- gset[[idx]]
Error: object 'gset' not found

>  sessionInfo()
R version 3.2.0 (2015-04-16)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1

locale:
[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252   
[3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C                          
[5] LC_TIME=English_United States.1252    

attached base packages:
[1] parallel  stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] XML_3.98-1.3         RCurl_1.95-4.7       bitops_1.0-6         limma_3.24.12        GEOquery_2.34.0     
[6] BiocInstaller_1.18.3 Biobase_2.28.0       BiocGenerics_0.14.0 

loaded via a namespace (and not attached):
[1] tools_3.2.0

It is working now with the same code.

Thanks,

Anita

I have the same problem!

I tried to run the R script in my PC and comes with an error after gset, I already emailed GEO to check the code or something.

The R script above is the exact copy of the generated script in GEO2R, but only works a few commands, if somebody has the same problem and could solve it, it will be very good if people share ir!

library(Biobase)
library(GEOquery)
library(limma)

# load series and platform data from GEO

gset <- getGEO("GSE7696", GSEMatrix =TRUE)
if (length(gset) > 1) idx <- grep("GPL570", attr(gset, "names")) else idx <- 1
gset <- gset[[idx]]

# make proper column names to match toptable
fvarLabels(gset) <- make.names(fvarLabels(gset))

# group names for all samples
sml <- c("X","X","X","G1","X","X","X","X","X","X","X","X","X","X","X","X","G0","X","X","X","X","X","X","X","X","X","X","X","X","X","X","X","X","X","X","X","X","X","X","X","X","X","X","X","X","X","X","X","X","X","X","X","X","X","X","X","X","X","X","X","X","X","X","X","X","X","X","X","X","X","X","X","X","X","X","X","X","X","X","X","X","X","X","X");

# eliminate samples marked as "X"
sel <- which(sml != "X")
sml <- sml[sel]
gset <- gset[ ,sel]

# log2 transform
ex <- exprs(gset)
qx <- as.numeric(quantile(ex, c(0., 0.25, 0.5, 0.75, 0.99, 1.0), na.rm=T))
LogC <- (qx[5] > 100) ||
          (qx[6]-qx[1] > 50 && qx[2] > 0) ||
          (qx[2] > 0 && qx[2] < 1 && qx[4] > 1 && qx[4] < 2)
if (LogC) { ex[which(ex <= 0)] <- NaN
  exprs(gset) <- log2(ex) }

--------------------------------------------------------------- until here It was working a few days ago, and the next code doesnt work

# set up the data and proceed with analysis
fl <- as.factor(sml)
gset$description <- fl
design <- model.matrix(~ description + 0, gset)
colnames(design) <- levels(fl)
fit <- lmFit(gset, design)
cont.matrix <- makeContrasts(G1-G0, levels=design)
fit2 <- contrasts.fit(fit, cont.matrix)
fit2 <- eBayes(fit2, 0.01)
tT <- topTable(fit2, adjust="fdr", sort.by="B", number=250)

# load NCBI platform annotation
gpl <- annotation(gset)
platf <- getGEO(gpl, AnnotGPL=TRUE)
ncbifd <- data.frame(attr(dataTable(platf), "table"))

# replace original platform annotation
tT <- tT[setdiff(colnames(tT), setdiff(fvarLabels(gset), "ID"))]
tT <- merge(tT, ncbifd, by="ID")
tT <- tT[order(tT$P.Value), ]  # restore correct order

tT <- subset(tT, select=c("ID","adj.P.Val","P.Value","t","B","logFC","Gene.symbol","Gene.title"))
write.table(tT, file=stdout(), row.names=F, sep="\t")