Dear members,

I have encountered some problems using XPS library on Mouse Gene 1.0 ST
arrays.. Basically, when I run rma on my cel files, the signal matrix only
have 21 rows (probeset?) for all the samples.  Has anybody here had the same
problem before?

## Generate the Scheme file

scmdir <- paste(.path.package("xps"),"schemes",sep="/")

libdir <- "./Affy/libraryfiles"

anndir <- "./Affy/Annotation"


scheme.moge10stv1r4.na31 <- import.exon.scheme("Scheme_MoGe10stv1r4_na31",
filedir=scmdir,                            layoutfile=paste(libdir,
"MoGene-1_0-st-v1.r4.clf",sep="/"),schemefile=paste(libdir,
"MoGene-1_0-st-v1.r4.pgf",sep="/"), probeset=paste(anndir,
"MoGene-1_0-st-v1.na31.mm9.probeset.csv",sep="/"),
transcript=paste(anndir,"MoGene-1_0-st-v1.na31.mm9.transcript.csv",sep="/"))


### Generate the signal file


celDir <- "./rawData/tissues/MoGene-1-0-st-v1/"

celfiles <- c("001.CEL","002.CEL","003.CEL")

celNames <- c("01","02","03")

datdir <-"rootData"


data.moge <- import.data(scheme.moge10stv1r4.na31,"mogene_glio",filedir=
datdir,celdir=celDir,celfiles=celfiles,celnames =celNames,verbose=T)


data.moge <- attachInten(data.moge)

tmp <- intensity(data.moge)

head(tmp)

> dim(tmp)

[1] 1102500       5


### So far so good,   I have

#### Problem starts here

data.rma <-rma(data.moge, "tmp_MoGene_Glio_RMA",filedir=datdir,tmpdir="",
option ="transcript", background="antigenomic",normalize=TRUE,exonlevel=
"all",verbose=TRUE,xps.scheme=scheme.moge10stv1r4.na31)


Creating new temporary file <rootData/tmp_MoGene_Glio_RMA.root>...

Opening file
</Library/Frameworks/R.framework/Resources/library/xps/schemes/Scheme_MoGe10stv1r4_na31.root>
in <READ> mode...

Opening file <./rootData/mogene_glio_cel.root> in <READ> mode...

Added <3> trees to PreprocesSet.

Preprocessing data using method <preprocess>...

   Background correcting raw data...

      setting selector mask for typepm <16316>

      calculating background for <01.cel>...

      background statistics:

         1087986 cells with minimal intensity 0

         970 cells with maximal intensity 84.8093

      calculating background for <02.cel>...

      background statistics:

         1087986 cells with minimal intensity 0

         4596 cells with maximal intensity 82.8614

      calculating background for <03.cel>...

      background statistics:

         1087986 cells with minimal intensity 0

         3018 cells with maximal intensity 71.3567

   Normalizing raw data...

      normalizing data using method <quantile>...

      setting selector mask for typepm <16316>

         finished filling <3> arrays.

         computing common mean...

         finished filling <3> trees.

   Converting raw data to expression levels...

      summarizing with <medianpolish>...

      setting selector mask for typepm <16316>

      setting selector mask for typepm <16316>

      calculating expression for <21> of <35556> units...Finished.

      expression statistics:

         minimal expression level is <36.657>

         maximal expression level is <14222.3>

   preprocessing finished.

Opening file
</Library/Frameworks/R.framework/Resources/library/xps/schemes/Scheme_MoGe10stv1r4_na31.root>
in <READ> mode...

Opening file <rootData/tmp_MoGene_Glio_RMA.root> in <READ> mode...

Opening file <rootData/tmp_MoGene_Glio_RMA.root> in <READ> mode...

Exporting data from tree <*> to file <rootData/tmp_MoGene_Glio_RMA.txt>...

Reading entries from <MoGene-1_0-st-v1.ann> ...Finished

<21> of <21> records exported.

>

>

>

> dim(tmp)

Error: object 'tmp' not found

>

> data.moge <- attachInten(data.moge)

tmp <- intensity(data.moge)

head(tmp)




> tmp <- intensity(data.moge)

> head(tmp)

  X Y 01.cel_MEAN 02.cel_MEAN 03.cel_MEAN

1 0 0        6213        8575        6339

2 1 0         105         198         126

3 2 0        6361        8720        6278

4 3 0         138         170         120

5 4 0         138         180         134

6 5 0         127         139         133

>

>

>

> dim(tmp)

[1] 1102500       5

>

>

> data.rma <-rma(data.moge,
"tmp_MoGene_Glio_RMA",filedir=datdir,tmpdir="",option ="transcript",
background="antigenomic",normalize=TRUE,exonlevel="all",verbose=TRUE,xps.scheme=scheme.moge10stv1r4.na31)

Creating new temporary file <rootData/tmp_MoGene_Glio_RMA.root>...

Opening file
</Library/Frameworks/R.framework/Resources/library/xps/schemes/Scheme_MoGe10stv1r4_na31.root>
in <READ> mode...

Opening file <rootData/mogene_glio_cel.root> in <READ> mode...

Added <3> trees to PreprocesSet.

Preprocessing data using method <preprocess>...

   Background correcting raw data...

      setting selector mask for typepm <16316>

      calculating background for <01.cel>...

      background statistics:

         1087986 cells with minimal intensity 0

         970 cells with maximal intensity 84.8093

      calculating background for <02.cel>...

      background statistics:

         1087986 cells with minimal intensity 0

         4596 cells with maximal intensity 82.8614

      calculating background for <03.cel>...

      background statistics:

         1087986 cells with minimal intensity 0

         3018 cells with maximal intensity 71.3567

   Normalizing raw data...

      normalizing data using method <quantile>...

      setting selector mask for typepm <16316>

         finished filling <3> arrays.

         computing common mean...

         finished filling <3> trees.

   Converting raw data to expression levels...

      summarizing with <medianpolish>...

      setting selector mask for typepm <16316>

      setting selector mask for typepm <16316>

      calculating expression for <21> of <35556> units...Finished.

      expression statistics:

         minimal expression level is <36.657>

         maximal expression level is <14222.3>

   preprocessing finished.

Opening file
</Library/Frameworks/R.framework/Resources/library/xps/schemes/Scheme_MoGe10stv1r4_na31.root>
in <READ> mode...

Opening file <rootData/tmp_MoGene_Glio_RMA.root> in <READ> mode...

Opening file <rootData/tmp_MoGene_Glio_RMA.root> in <READ> mode...

Exporting data from tree <*> to file <rootData/tmp_MoGene_Glio_RMA.txt>...

Reading entries from <MoGene-1_0-st-v1.ann> ...Finished

<21> of <21> records exported.


> expr.rma <- validData(data.rma)

> dim(expr.rma)

[1] 21  3


## only 21 records....


Can anyone help? Thank you!


Zach Liu


Genomics & Computational Biology Program
Abramson Cancer Institute, School of Medicine
University of Pennsylvania

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