Question: oligo package requires the annotation package pd.ht.mg.430.pm - where is it?
0
gravatar for peer.karmaus
4.2 years ago by
United States
peer.karmaus0 wrote:

Hi Everyone,

I recently had to reformat my mac to get the OSX Yosemite. Now I run into the problem that the oligo package does not work.

The reason seems to be that for the .CEL files that I am using (at the read.celfiles step) the oligo package requires the annotation package pd.ht.mg.430.pm, which is not in the repository (anymore?): https://www.bioconductor.org/packages/release/data/annotation/

Has anybody run into this problem? The 430 PM it is a very common affymetrix platform that did not cause any problems in the oligo package before (I am using unchanged R script that was previously working).
http://www.affymetrix.com/catalog/131444/AFFY/HT+MG-430+PM+Array+Plate#1_3

 

Any comments/suggestions are welcomed. I am on the brink of trying figuring out how to build my own annotation package from here:http://www.bioconductor.org/packages/release/bioc/vignettes/pdInfoBuilder/inst/doc/BuildingPDInfoPkgs.pdf

 

Thanks!

Peer

 

microarray annotation oligo • 1.3k views
ADD COMMENTlink modified 4.2 years ago by James W. MacDonald52k • written 4.2 years ago by peer.karmaus0

There is a package called pd.ht.mg.430a; is that the one you are looking for?

http://www.bioconductor.org/packages/release/data/annotation/html/pd.ht.mg.430a.html

ADD REPLYlink written 4.2 years ago by Dan Tenenbaum8.2k

Thanks for the reply, but no unfortunately that is not it. It may be similar enough with the same annotation but the oligo package specifically asks for "pd.ht.mg.430.pm", while it loads the "pd.ht.mg.430a" annotation just fine.

ADD REPLYlink written 4.2 years ago by peer.karmaus0

Here's the full error code:

> affyRaw <- read.celfiles(celFiles)
Loading required package: pd.ht.mg.430.pm
Attempting to obtain 'pd.ht.mg.430.pm' from BioConductor website.
Checking to see if your internet connection works...
Package 'pd.ht.mg.430.pm' was not found in the BioConductor repository.
The 'pdInfoBuilder' package can often be used in situations like this.
Error in read.celfiles(celFiles) :
  The annotation package, pd.ht.mg.430.pm, 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.ht.mg.430.pm’

ADD REPLYlink written 4.2 years ago by peer.karmaus0

It says that pdInfoBuilder can help you. Perhaps you can use pdInfoBuilder to create the package you need. I don't know much about it but perhaps someone else can chime in.

http://bioconductor.org/packages/release/bioc/html/pdInfoBuilder.html

ADD REPLYlink written 4.2 years ago by Dan Tenenbaum8.2k

Thanks! That was going to be my last resort. I linked the pdInfoBuilder at the end of the original post, too. 

ADD REPLYlink written 4.2 years ago by peer.karmaus0
Answer: oligo package requires the annotation package pd.ht.mg.430.pm - where is it?
0
gravatar for James W. MacDonald
4.2 years ago by
United States
James W. MacDonald52k wrote:

To build the package using pdInfoBuilder, you need the pgf and clf files, which I can't find. The obvious (and simpler) way to analyze these arrays is to use the affy package instead.
 

ADD COMMENTlink written 4.2 years ago by James W. MacDonald52k

Thanks for the input James! As far as I know, the new affy arrays cannot use the affy package: http://homer.salk.edu/homer/basicTutorial/affymetrix.html (see "Newer Affymetrix Arrays") - I went through this once before, is this not an issue anymore?

I did not find a .PGF or .CLF file either, however I found the CDF and annot.csv files, but I would still need the .CEL file (not sure if this can be any CEL file using this array or not – I contacted Affymetrix about this)

HT MG-430 PM (.CDF): http://www.affymetrix.com/Auth/support/downloads/library_files/HT_MG-430_PM_rev05.zip

HT MG-430 PM (.CSV): http://www.affymetrix.com/Auth/analysis/downloads/na35/ivt/HT_MG-430_PM.na35.annot.csv.zip

The problem remains that the pdInfoBuilder package builds libraries using preset slots. So I either need the .PDG and .CLF OR the .CEL with the above two files.

ADD REPLYlink written 4.2 years ago by peer.karmaus0
1

The mouse 430 arrays are not new arrays! These are old 3'-biased arrays, for which the affy package was designed. This has never been an issue, so I don't know what you went through before. Trust me - use the affy package.

ADD REPLYlink written 4.2 years ago by James W. MacDonald52k

Thanks James! I used the affy package and it worked. Not sure what was the problem before.

ADD REPLYlink written 4.2 years ago by peer.karmaus0

I tried the affy package with some newer data (non-GEO) and I got the following error:

The affy package is not designed for this array type.
Please use either the oligo or xps package.

That was the initial reason I migrated to the oligo package, where the package "pd.ht.mg.430.pm" is missing from the bioconductor repository and is necessary to analyze the files of this array type.

So... affy sometimes works, but not for all affy arrays including the Mouse Gene 2.0 ST

ADD REPLYlink written 4.2 years ago by peer.karmaus0

Well, that's true. When Affy first came out with their 3'-biased arrays, the array designs were very simple. Each probe was part of a single probeset, so all you had to do was map the probes to probesets, and then summarize the data within each probeset.

In more recent years, the Affy arrays have become increasingly complex. A given probe may be used in multiple probesets (including paradoxically both 'main' probesets as well as control probesets). This is true of things like the Gene 2.0 ST arrays. Rather than trying to extend the affy package to be able to handle these increasingly complex designs, Rafa and Benilton developed an entirely new pipeline intended to work for any oligonucleotide based array, namely the oligo/pdInfoBuilder pipeline.

Despite multiple attempts (by me) on its life, the affy package is still kicking around, because people love them some affy package, and in truth it is useful for the old arrays and those who use them, even though we end up with confused end users who don't know which to use and why.

As an aside you CAN use oligo/pdInfoBuilder for the old 430 arrays, and I show how to do so A: How to use brainarray custom cdf with oligo package?. But going through all the steps to use a CDF file when you can just use the affy package seems like a bad cost/benefit situation.

ADD REPLYlink written 4.2 years ago by James W. MacDonald52k
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