[BioC] Reading SMD data in limma

[Audrey Kauffmann]

Dear Rohit,

Regarding your first question about the use of the ArrayExpress
package, the error message indicated to try to set the rawcol argument
using the names listed. For instance, you could try:
> data = ArrayExpress("E-SMDB-1428", rawcol = list(R="ScanAlyze:RESULT.CH2I_MEAN", G"ScanAlyze:RESULT.CH1I_MEAN", Rb="ScanAlyze:RESULT.CH2B_MEDIAN", Gb="ScanAlyze:RESULT.CH1B_MEDIAN"))

The output is a list of two NChannelSet because one of the file has a
different format as Gordon mentionned.

Best wishes,
Audrey

2010/6/10 Gordon K Smyth <smyth at wehi.edu.au>:
> 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
>
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-- 
Audrey Kauffmann
Bergonie Cancer Institute
229 Cours de l'Argonne
33076 Bordeaux
France
+33.5.56.33.04.53