Question: Problem in processing microarray data with HuEx-1_0-st-v1 platform
0
gravatar for ashuein
11 days ago by
ashuein0
ashuein0 wrote:

When I am trying to process a micro-array data with Array Express id E-GEOD-21298, I get the following error:

Code Run:

  >celFile<-list.celfiles(full.names=TRUE)
  >rawDat<- read.celfiles(celFile)
  >norDat<- oligo::rma(rawDat,background=TRUE,normalize=TRUE,target="core")

Platform design info loaded.
Reading in : ./GSM532260.CEL
Reading in : ./GSM532261.CEL
Reading in : ./GSM532262.CEL
Reading in : ./GSM532263.CEL
Reading in : ./GSM532264.CEL
Reading in : ./GSM532265.CEL
Reading in : ./GSM532274.CEL
Reading in : ./GSM532277.CEL
Reading in : ./GSM532278.CEL
Reading in : ./GSM532279.CEL
[1] "pd.huex.1.0.st.v2"
Background correcting
Normalizing
Calculating Expression
  **Error in (function (classes, fdef, mtable)  : 
      unable to find an inherited method for function ‘columns’ for signature ‘"AffyExonPDInfo"’**

I am unable to understand this error. Any help with this error ?


Also, this array belongs to HuEx-1_0-st-v1 while the current available annotation package in Bioconductor is HuEx-1_0-st-v2 . [Which might be the reason of above error] Running the command:

biocLite("pd.huex.1.0.st.v1")

gives error:

package ‘pd.huex.1.0.st.v1’ is not available (for R version 3.4.4)

So how do I annotate the processed files for the older version ?

ADD COMMENTlink modified 8 days ago by Kevin Blighe21k • written 11 days ago by ashuein0

See if these notes help. That link came from this thread.

ADD REPLYlink written 11 days ago by genomax50k
1
gravatar for Kevin Blighe
8 days ago by
Kevin Blighe21k
University College London Cancer Institute
Kevin Blighe21k wrote:

There have indeed been issues with this array's annotation package. There is further discussion here: pd.huex.1.0.st.v2 package doubt.

What you should do is download the CDF from GenoMax's first link - you will require a login for Affymetrix and then, also, to unzip the downloaded file. Then set it up as a custom CDF by following this tutorial: How To Install A Specific Cdf Package For Use In Bioconductor

Once you have it set up, you can then explicitly specify it by following my code here ( C: [HuEx-1_0-st] Affymetrix Human Exon 1.0 ST Array [transcript (gene) version] ) and at the line:

project <- read.celfiles(CELFiles, package="HuEx-1_0-st-v2-cdf")

If you don't specify 'package', here, then the function will just attempt to download the erronous package yet again. It even failed on my computer.

To then deal with annotation isssues, you can download the CSV annotations from here: ( http://www.affymetrix.com/support/technical/byproduct.affx?product=huexon-st ) and then manually annotate your probes, as I do here: C: [HuEx-1_0-st] Affymetrix Human Exon 1.0 ST Array [transcript (gene) version]

By the way, I'm not sure why you were trying to install via biocLite() 'pd.huex.1.0.st.v1' when these arrays are actually 'pd.huex.1.0.st.v2'.

Kevin

ADD COMMENTlink written 8 days ago by Kevin Blighe21k
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