[BioC] Selecting Unique rows in multiple column data frames

[alex lam (RI)]

Hi Matjaz,
For option 1, have a look at the help page of the method "aggregate".

I don't understand your option 2. Perhaps I am misreading what your are saying.
If you want to select unique rows according to column 1 and 2, you can create a third column by joining col1 and 2

Col3 <- paste(ID, M, sep="_")
Index <- unique(Col3)  
YourData[Index,]

But I can't see that any replicates would be having identical M values. 

Cheers,
Alex

------------------------------------
Alex Lam
PhD student
Department of Genetics and Genomics
Roslin Institute (Edinburgh)
Roslin
Midlothian EH25 9PS
Great Britain

Phone +44 131 5274471
Web   http://www.roslin.ac.uk


-----Original Message-----
From: bioconductor-bounces at stat.math.ethz.ch [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Matjaž Hren
Sent: 06 November 2006 09:06
To: Bioconductor
Subject: [BioC] Selecting Unique rows in multiple column data frames

Dear list!

 

I have data frames with 2 columns of normalised microarray data (more that 10k rows, custom-made array) with the following layout (not real data):

 

ID        M

ID1      -4.60138

ID2      -3.28832

ID3      4.83560

ID4      6.45286

ID4      6.65235

ID4      6.38745

ID4      6.74514

ID5      4.43995

ID6      -1.78943

ID7      -4.00257

ID8      -4.46327

ID9      -3.13956

ID10    2.52233

ID11    -1.81214

ID11    -1.78625

ID11    -1.61214

ID11    -1.52354

 

ID is the oligo ID (spot-ID), M is the corresponding M-value.

 

Only one spot per block is present in replicates (4). Therefore I would like to use one of the following 2 options:

 

1. Average the M-values in rows that have the same ID and extract the data table with both columns.

2. or if the first option does not work: Extract the rows with unique ID (both columns) and remove the replicates. I tried using "unique" on ID column but I couldn't extend its use to more than one column in the data frame.

 

I used R 2.4.0 and limma package for normalisation.

 

 

Thank you in advance,

 

 

Matjaz

 

----------------------------------------------------------------------------

Matjaz Hren

 

National Institute of Biology

Department of Plant Physiology and Biotechnology

SLOVENIA

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