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affymetrix miRNA microarray analysis,

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.

r microarray mir annotation package
• 3,556 views • link
written by english.server english.server

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

• 0 views • link
written by Kevin Blighe Kevin Blighe

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

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written by GenoMax GenoMax

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.
• 0 views • link
written by english.server english.server

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.

• 0 views • link
written by Kevin Blighe Kevin Blighe

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

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written by english.server english.server

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

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written by GenoMax GenoMax

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’
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written by english.server english.server

Can you install the pdInfoBuilder package and then retry?

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written by Kevin Blighe Kevin Blighe

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

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written by english.server english.server

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