[BioC] Reading SMD data in limma

[Gordon K Smyth]

Dear Rohit,

The problem appears to be that your data files have different numbers of 
rows.  The first 7 files have the same number of rows, but then the 8th 
file is different.  Try this:

   x1 <- read.maimages(files=filelist[1:7],...
   x2 <- read.maimages(files=filelist[8],...

   dim(x1)
   dim(x2)

Best wishes
Gordon

> Date: Wed, 9 Jun 2010 12:57:33 +0530
> From: Rohit Farmer <rohit.farmer at gmail.com>
> To: bioconductor <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 and used the
> following command .... but getting this error and the object is not being
> created ..
>
>
> data <- read.maimages(files=filelist, source="smd",
> columns=list(R="ScanAlyze:RESULT.CH1I_MEAN",G="ScanAlyze:RESULT.CH2I_MEAN",Rb="ScanAlyze:RESULT.CH1B_MEDIAN",Gb="ScanAlyze:RESULT.CH2B_MEDIAN"))
> Read E-SMDB-1428-raw-data-516957410.txt
> Read E-SMDB-1428-raw-data-516957425.txt
> Read E-SMDB-1428-raw-data-516957442.txt
> Read E-SMDB-1428-raw-data-516957457.txt
> Read E-SMDB-1428-raw-data-516957472.txt
> Read E-SMDB-1428-raw-data-516957490.txt
> Read E-SMDB-1428-raw-data-516957507.txt
> Error in RG[[a]][, i] <- obj[, columns[[a]]] :
>  number of items to replace is not a multiple of replacement length
>
>
> Please help to sort this problem
>
> Regard
> rohit
> -- 
> Rohit Farmer
> M.Tech Bioinformatics
> Department of Computational Biology and Bioinformatics
> Jacob School of Biengineering and Biotechnology
> Sam Higginbottom Institute of Agriculture, Technology and Sciences
> (Formerly known as Allahabad Agricultural Institute - Deemed University)
> Allahabad, UP, INDIA - 211 007
> Ph. No. 9839845093, 9415261403
> e-Mail rohit.farmer at gmail.com
> Blog http://rohitsspace.blogspot.com

______________________________________________________________________
The information in this email is confidential and intend...{{dropped:4}}