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)
•
written
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kalyanimeha •
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.
So, how can I find out up and downregulated gene from gse34747 by using limma or any other package?
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.
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have you forgot to make the
datadirectory?before all do
dir.create("data")After creating directory previous errors got solved...thanks for helping out. Getting error while calculating ttest.
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
Warning message:
NaNs produced
Error in rowcoltt(x, fac, tstatOnly, 1L) :
Number of groups is 6, but must be >0 and <=2 for 'rowttests'.
the data looks like it's already transformed