Question: Differential Expression fro GEO Data
0
gravatar for kalyanimeha
23 months ago by
kalyanimeha30
New Delhi INDIA
kalyanimeha30 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 • 611 views
ADD COMMENTlink modified 23 months ago by Sean Davis25k • written 23 months ago by kalyanimeha30

have you forgot to make the data directory?

ADD REPLYlink written 23 months ago by russhh5.1k

before all do dir.create("data")

ADD REPLYlink written 23 months ago by egeulgen980

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 23 months ago • written 23 months ago by kalyanimeha30

the data looks like it's already transformed

ADD REPLYlink written 23 months ago by russhh5.1k
1
gravatar for Sean Davis
23 months ago by
Sean Davis25k
National Institutes of Health, Bethesda, MD
Sean Davis25k 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 23 months ago by Sean Davis25k

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

ADD REPLYlink written 23 months ago by kalyanimeha30
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 23 months ago by Sean Davis25k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1323 users visited in the last hour