[BioC] [marray] Importing SMD files into marray

[Wu, Zhuang]

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