[BioC] Adding annotations to fit2

[James MacDonald]

Hi Sally,

Your fit2 object is of class MArrayLM, whereas MGLnew is a data.frame, so there is no clear path to merge the two (in general, I believe merge() expects things of the same class, probably data.frame).

You might have better luck writing out your fit2 object using write.fit(), then reading back in using read.table(). This will give you a data.frame that you could then probably merge() with your MGLnew data.frame.

Best,

Jim


James W. MacDonald, M.S.
Biostatistician
Hildebrandt Lab
8220D MSRB III
1150 W. Medical Center Drive
Ann Arbor MI 48109-0646
734-936-8662
>>> "Sally" <sagoldes at shaw.ca> 02/16/09 10:35 PM >>>
I want merge fit2 with a txt file I'll call MGL (mastergenelist) which contains gene id information.  I am using a custom cDNA array.  The reason is that I want the gene ID information along-side the rownames (which are the accession IDs).  Both have identical row names.  MGL has missing data.

I have tried:

MGLnew<-read.table(file="MGL.txt",sep="\t",header=TRUE,na.strings="",fill=TRUE)  #WORKS
write.table(MGLnew,file="MGLnew.txt",sep="\t") #WORKS
fit2<-merge(fit2,MGLnew,by="row.names")  #NOT WORKING

When I run this I get the following error message:

Error in dim(data) <- dim : attempt to set an attribute on NULL

What does this error message mean?  How do I fix the problem?

Sally Goldes

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