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Question: Affymetrix miRNA4.1 / oligo package / pd.mirna.4.1
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gravatar for rolan.zauner
18 months ago by
rolan.zauner10
rolan.zauner10 wrote:

Dear Bioconductor community,

  I was wondering if anyone could give me hint to where I can find pd.mirna.4.1 for affymetrix miRNA4.1 (array plate platform) microarray chip to read .cel files? Currently I can only find pd.mirna.4.0 (single chip array platform) on bioconductor.

Alternatively I would be happy if anyone has .pgf and .clf files which I could use in combination with the PDInfoBuilder library to generate a pd.mirna.4.1 database my own.

Many thx for your ideas!

cheers roland

ADD COMMENTlink modified 18 months ago • written 18 months ago by rolan.zauner10
3
gravatar for James W. MacDonald
18 months ago by
United States
James W. MacDonald48k wrote:

You can get them from ThermoFisher. You want the library files for Expression Console and AGCC, not the ones for TAC.

ADD COMMENTlink written 18 months ago by James W. MacDonald48k

Thx James, I've already contacted TF, let's see how responsive they are :-)

ADD REPLYlink written 18 months ago by rolan.zauner10
1
gravatar for rolan.zauner
18 months ago by
rolan.zauner10
rolan.zauner10 wrote:

With the .pgl and .clf files from the ThermoFisher link provided by James I've been able to create the desired pd.mirna.4.1 library :-)

 

######################################################
# Building Annotation Packages with pdInfoBuilder    #
# for Use with the oligo Package / Benilton Carvalho #
# -------------------------------------------------- #
# TF/affymetrix miRNA4.1 array plate                 #
# .pgf and .clf files download on 14.06.2017 from:   #
# https://tools.thermofisher.com/content/sfs...      #
# /supportfiles/mirna_4_sample_data.zip              #
# pd.mirna.4.1 (v0.1)                                #
######################################################


source("https://bioconductor.org/biocLite.R")
biocLite("pdInfoBuilder")

library("pdInfoBuilder")
pgfFile <- "miRNA-4_1-st-v1.pgf"
clfFile <- "miRNA-4_1.clf"
csvAnnoFile=csvAnno
 
pkg <- new("AffyMiRNAPDInfoPkgSeed",
            version="0.1",
            author="ZaRo", email="",
            biocViews="AnnotationData",
            genomebuild="NCBI Build 35, May 2004",
            pgfFile=pgfFile, clfFile=clfFile)
 
makePdInfoPackage(pkg, destDir=".")


library(devtools)
build("pd.mirna.4.1")

# install library
# library("pd.mirna.4.1")

 

 

ADD COMMENTlink written 18 months ago by rolan.zauner10
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