Question: affymetrix miRNA microarray analysis,
0
gravatar for english.server
14 months ago by
Germany
english.server140 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 14 months ago by english.server140

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

ADD REPLYlink written 14 months ago by Kevin Blighe42k
2

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

ADD REPLYlink written 14 months ago by genomax67k
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 14 months ago by Kevin Blighe42k

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 14 months ago • written 14 months ago by english.server140

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 14 months ago by Kevin Blighe42k

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 14 months ago by english.server140

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

ADD REPLYlink written 14 months ago by genomax67k

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 14 months ago by english.server140

Can you install the pdInfoBuilder package and then retry?

ADD REPLYlink written 14 months ago by Kevin Blighe42k

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

ADD REPLYlink written 14 months ago by english.server140
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