[BioC] Reading SMD data in limma

Gordon K Smyth smyth at wehi.EDU.AU
Mon Jun 21 01:27:39 CEST 2010

Dear Budhayash,

You cannot combine arrays 1-7 with arrays 9-16 unless they have the same 
probes.  So you need to figure out which are the extra probes in arrays 
1-7 and remove them (by subsetting the RG object you've read in).  Then 
you can use cbind() to put the first and second groups together.

We have no control over what authors put on ArrayExpress, so there is no 
general solution.  It is not possible to give more specific advice, such 
as code examples, from the information you give.

Best wishes

Associate Professor Gordon K Smyth,
NHMRC Senior Research Fellow,
Bioinformatics Division, 
Walter and Eliza Hall Institute of Medical Research, 
1G Royal Parade, Parkville, Vic 3052, Australia.
smyth at wehi.edu.au

> Date: Fri, 18 Jun 2010 16:34:50 +0530
> From: Budhayash Gautam <budhayashgautam at gmail.com>
> To: bioconductor at stat.math.ethz.ch
> Subject: [BioC] Reading SMD data in limma
> Hello everyone ... i am trying to make an object from an SMD data 
> downloaded from ArrayExpress ... using the limma package .. but getting 
> this error and the object is not being created ...... number of items to 
> replace is not a multiple of replacement length.
> The problem appears to be that data files (total 16 files) have
> different numbers of rows.  All the files have the same number of rows
> (5337 rows), but only the 8th file is different (4993 rows). how these
> rows can be made similar in number so that all files can be changed to
> a single object.
> how can i deal with this situation. if we read files (1-7 & 9-16) and
> 8 separately  then two objects will be created then how can these two
> objects be merged for further analysis.
> Please help to sort this problem
> Regard
> -- 

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