[BioC] [marray] Importing SMD files into marray

[Furge, Kyle]

If you are able to read one file at a time, but not as a collection, it may
be that the arrays are from different print runs and the dimensions of the
arrays are not be exactly the same.

The last time I remember looking at this, the .xls header contains the
printrun identifier.  In addition, if you downloaded the experiment archive,
it should contain information (i.e. .gal files) for each printrun used.

Maybe look at the 18195 and 19938 arrays and determine if the layout is
exactly the same.

While not trival, a search of the BioC mailing list will give some options
into combining data from different platforms into a single data set.  I
guess I would start with seeing if I could load a batches of files from the
same print run and go from there.

-kyle

> From: "Wu, Zhuang" <ZWU3 at PARTNERS.ORG>
> Date: Mon, 9 Jan 2006 12:49:54 -0500
> To: <bioconductor at stat.math.ethz.ch>
> Subject: [BioC]  [marray] Importing SMD files into marray
> 
> 
> Hi, I am trying to import a bunch of SMD files(64 files) which are from a
> single
> mocroarray chip. The following is what I did and what I got:
> 
> 1. I started R in the directory that has all the .xls files
> 2. library("marray")
> 3. read.SMD("18195.xls"), returned:
> 
>> read.SMD("18195.xls")
> Generating target sample info from all files
> Reading ...  ./18195.xls
> An object of class "marrayRaw"
> @maRf
> [1]  2478  2705  6402  3182 10273
> 45691 more rows ...
> 
> @maGf
> [1]  3891  4776 10829  5665 21048
> 45691 more rows ...
> 
> @maRb
> [1] 356 342 351 351 348
> 45691 more rows ...
> 
> @maGb
> [1] 235 256 252 255 242
> 45691 more rows ...
> 
> @maW
> <0 x 0 matrix>
> 
> @maLayout
> An object of class "marrayLayout"
> @maNgr
> [1] 12
> 
> @maNgc
> [1] 4
> 
> @maNsr
> [1] 32
> 
> @maNsc
> [1] 30
> 
> @maNspots
> [1] 46080
> 
> @maSub
> [1] TRUE TRUE TRUE TRUE TRUE
> 46075 more elements ...
> 
> @maPlate
> factor(0)
> Levels:
> 
> @maControls
> factor(0)
> Levels:
> 
> @maNotes
> character(0)
> 
> 
> @maGnames
> An object of class "marrayInfo"
> @maLabels
> [1] "1" "2" "3" "4" "5"
> 45691 more elements ...
> 
> @maInfo
>       Name     Clone.ID
> X13834 13834 IMAGE:342721
> X13846 13846 IMAGE:233721
> X13929 13929  IMAGE:50754
> X13941 13941 IMAGE:126243
> X14025 14025 IMAGE:234736
> 45691 more rows ...
> 
> @maNotes
> [1] ""
> 
> 
> @maTargets
> An object of class "marrayInfo"
> @maLabels
> [1] "18195"
> 
> @maInfo
>                   Experiment           Cy3         Cy5 SlideName
> 1 BC91_minusTS_Bio-6_RNAeasy_1 Stratagene_aT BC-D-091_aT   shbg054
> 
> @maNotes
> character(0)
> 
> 
> @maNotes
> [1] ""
> 
> 4. read.SMD() (I tried to read all files), returned:
> 
>> read.SMD()
> Generating target sample info from all files
> Reading ...  ./18195.xls
> Reading ...  ./19938.xls
> Error in "[<-"(`*tmp*`, , f, value = c(551, 167, 1617, 147, 2088, 153,  :
>       number of items to replace is not a multiple of replacement length
>> 
> 
> 
> It seems that I can read in one file at a time (just like what I did
> read.SMD("18195.xls")), but I need to grab all the files together. Anyone has
> any idea? I am using R 2.2.0 on Linux. Thanks in advance!
> 
> Kind regards,
> 
> Zhuang Wu
> 
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