[BioC] Adding annotations to fit2 - still having problems

[Sally]

Hello,

I am using Limma for microarray analysis.  Ultimately I want to 
add/combine/append (not sure what word is correct) a file named MGL.txt 
(mastergene list) to fit2 so that when topTable prints it will have the 
annotation information for each gene.  The first few lines of MGL.txt looks 
like this (there are blank cells/missing data).  There are 17,328 rows and 6 
columns in this file.

     well accession bitscore evalue symbol
      U179971039 GFP
      empty1 Blank Well
      empty2 Blank Well
      empty3 Blank Well
      empty4 Blank Well
      empty5 Blank Well
      empty6 Blank Well
      empty7 Blank Well
      empty8 Blank Well
      CA054869 UNKNOWN
      CB490276 G2/mitotic-specific cyclin-B2 Q60FX9 524.24 3.58E-148 ccnb2
      CA769480 Endothelial differentiation-related factor 1 homolog Q6PBY3 
214.16 8.45E-55 edf1



MGL.txt was read in with:
MGLnew<-read.table(file="MGL.txt",sep="\t",header=TRUE,na.strings="",fill=TRUE,row.names=1)
When MGLnew is printed on screen it looks like this (first few lines)

              accession bitscore    evalue      symbol
U179971039         <NA>       NA        NA        <NA>
empty1             <NA>       NA        NA        <NA>
empty2             <NA>       NA        NA        <NA>
empty3             <NA>       NA        NA        <NA>
empty4             <NA>       NA        NA        <NA>
empty5             <NA>       NA        NA        <NA>
empty6             <NA>       NA        NA        <NA>
empty7             <NA>       NA        NA        <NA>
empty8             <NA>       NA        NA        <NA>
CA054869           <NA>       NA        NA        <NA>
CB490276         Q60FX9   524.24 3.58e-148       ccnb2
CA769480         Q6PBY3   214.16  8.45e-55        edf1


When I then check the # of rows using nrow(MGLnew) it says there are 3312 
rows, even though the original file had 17,328 rows.
Also it doesn't include the column "well" in MGLnew.


Why are these two things happening?

Sally Goldes








----- Original Message ----- 
From: "john seers (IFR)" <john.seers at bbsrc.ac.uk>
To: "Sally" <sagoldes at shaw.ca>; <bioconductor at stat.math.ethz.ch>
Sent: Tuesday, February 17, 2009 8:35 AM
Subject: RE: [BioC] Adding annotations to fit2




Hi Sally

Is fit2 by any chance the output from limma fitting a linear model? If
not this is not relevant.

If it is so I think you may be able to do something like

fit2$genes<-cbind(fit2$genes, MGLnew)

If that does not work, if you are using topTable a bit later, you can do
something like this:

       tt<-topTable(eb, number=ngenes, genelist=cbind(eb$genes, MGLnew))


       Regards
       John


---

-----Original Message-----
From: bioconductor-bounces at stat.math.ethz.ch
[mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Sally
Sent: 17 February 2009 03:35
To: bioconductor at stat.math.ethz.ch
Cc: Sally
Subject: [BioC] Adding annotations to fit2

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="",fil
l=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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