Question: Differential Expression fro GEO Data
0
gravatar for kalyanimeha
3.0 years ago by
kalyanimeha40
New Delhi INDIA
kalyanimeha40 wrote:

I am getting an error while downloading GEO matric series file from URL. But URL contains the matrix file.

library(GEOquery)

library(limma)

url <- "ftp://ftp.ncbi.nih.gov/pub/geo/DATA/SeriesMatrix/GSE34747/GSE34747_series_matrix.txt.gz"

filenm <- "data/GSE34747_series_matrix.txt.gz"

if(!file.exists(filenm)) download.file(url, destfile=filenm)

  • Error in download.file(url, destfile = filenm) : cannot open destfile 'data/GSE34747_series_matrix.txt.gz', reason 'No such file or directory'
rna-seq limma R geo • 822 views
ADD COMMENTlink modified 3.0 years ago by Sean Davis26k • written 3.0 years ago by kalyanimeha40

have you forgot to make the data directory?

ADD REPLYlink written 3.0 years ago by russhh5.5k

before all do dir.create("data")

ADD REPLYlink written 3.0 years ago by egeulgen1.1k

After creating directory previous errors got solved...thanks for helping out. Getting error while calculating ttest.

head(exprs(gse))

GSM854486 GSM854487 GSM854488 GSM854489 GSM854490 GSM854491

GT_44k_23_P100001 -1.06 -0.13 -3.44 -1.06 -0.10 -3.09

GT_44k_23_P100011 -3.26 -2.76 -2.54 -2.72 -2.77 -2.69

GT_44k_23_P100022 -1.80 -5.93 -6.03 -5.48 -6.56 -6.32

GT_44k_23_P100056 -3.43 -3.15 -2.35 -3.04 -3.17 -2.55

GT_44k_23_P100074 2.09 2.97 2.76 2.38 3.20 3.19

GT_44k_23_P100092 -1.88 -2.33 -1.39 -1.92 -2.14 -1.21

exprs(gse) <- log2(exprs(gse))

Warning message:

NaNs produced

boxplot(exprs(gse),outline=FALSE)

pd <- pData(gse)

SampleGroup <- pd$source_name_ch1

library(genefilter)

destats <- rowttests(exprs(gse),fac=SampleGroup)

Error in rowcoltt(x, fac, tstatOnly, 1L) :

Number of groups is 6, but must be >0 and <=2 for 'rowttests'.

ADD REPLYlink modified 3.0 years ago • written 3.0 years ago by kalyanimeha40

the data looks like it's already transformed

ADD REPLYlink written 3.0 years ago by russhh5.5k
1
gravatar for Sean Davis
3.0 years ago by
Sean Davis26k
National Institutes of Health, Bethesda, MD
Sean Davis26k wrote:

I would do something like:

gse = getGEO("GSE34747", destdir="data")[[1]]

Then, you should be able to use limma directly. Note that the data have already been log-transformed, so taking another log will result in the warnings you see above.

ADD COMMENTlink written 3.0 years ago by Sean Davis26k

So, how can I find out up and downregulated gene from gse34747 by using limma or any other package?

ADD REPLYlink written 3.0 years ago by kalyanimeha40
1

limma has a great user guide. I would suggest starting there. If you get stuck, you can ask a new question with the details of what you have tried.

ADD REPLYlink written 3.0 years ago by Sean Davis26k
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