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