Question: affymetrix miRNA microarray analysis,
0
gravatar for english.server
2.2 years ago by
Germany
english.server200 wrote:

Hi all!

I am new to microarray analysis, when I want to read in .CEL files, R tries to download a package and the package is not found. Here is the R output:

Package 'pd.mirna.1.0.2xgain' was not found in the BioConductor repository.

what should I do? Thank you in advance.

ADD COMMENTlink written 2.2 years ago by english.server200

Which microarray vendor (Affymetrix, Agilent, Illumina?) and version are you using? Are you trying to follow some tutorial?

ADD REPLYlink written 2.2 years ago by Kevin Blighe59k
2

Says affymetrix in title. It may be the GeneChip miRNA 4.0 array.

ADD REPLYlink written 2.2 years ago by genomax83k
1

Yes, take a look here in order to get the correct package name: https://www.bioconductor.org/packages/release/data/annotation/

Searc for 'pd.mirna.1.0' to take you down the list.

ADD REPLYlink written 2.2 years ago by Kevin Blighe59k

thank you. it is

[miRNA-1] Affymetrix Multispecies miRNA-1 Array

I installed pd.mirna.1.0 but R still says:

The annotation package, pd.mirna.1.0.2xgain, could not be loaded.
ADD REPLYlink modified 2.2 years ago • written 2.2 years ago by english.server200

I have just successfully installed and loaded it on R 3.2.5 using:

source("http://bioconductor.org/biocLite.R")
biocLite("pd.mirna.1.0")
require("pd.mirna.1.0")

Can you confirm your R version an how you have tried to install this package? Also, a restart of your computer can always help, followed by the installation and loading of the package when you first re-open R.

ADD REPLYlink written 2.2 years ago by Kevin Blighe59k

Thank you. I installed pd.mirna.1.0 but R still looks for 'pd.mirna.1.0.2xgain' as I run my code.

ADD REPLYlink written 2.2 years ago by english.server200

Then you need to show what code you are running to diagnose that part.

ADD REPLYlink written 2.2 years ago by genomax83k

Thanks. I've downloaded raw .cel files (4 cel files) from GSE49885, and put them in a folder called (G:\e\GSE49885_RAW) this is my code:

setwd ('G:\\e\\GSE49885_RAW')
library (oligo)
afbatch=read.celfiles(list.celfiles())

and R says

Loading required package: pd.mirna.1.0.2xgain
Attempting to obtain 'pd.mirna.1.0.2xgain' from BioConductor website.
Checking to see if your internet connection works...
Package 'pd.mirna.1.0.2xgain' was not found in the BioConductor repository.
The 'pdInfoBuilder' package can often be used in situations like this.
Error in read.celfiles(list.celfiles()) : 
  The annotation package, pd.mirna.1.0.2xgain, could not be loaded.
In addition: Warning message:
In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘pd.mirna.1.0.2xgain’
ADD REPLYlink written 2.2 years ago by english.server200

Can you install the pdInfoBuilder package and then retry?

ADD REPLYlink written 2.2 years ago by Kevin Blighe59k

Affymetrix Multispecies miRNA-1 Array. No I am not following any tutorials.

ADD REPLYlink written 2.2 years ago by english.server200
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