Hello bioc user,

I have found a new package for the quality analysis and preprocessing of
microarray data - xps.
Unfortunately it is not so easy to use.
I am working with the miRNA microarray from affymetrix.

I tried to work according to the xps vignette and everything went just fine,
up to the point where I wanted to analyze my own data...

First I couldn't create a root file, as there is no explanation as to how to
do it. I tried the command

miRNA.test <- import.expr.scheme("mirna",filedir=getwd(),


                     schemefile="miRNA-1_0_2Xgain.CDF",
                     probefile="miRNA-1_0_2Xgain_probe.tab",
                     annotfile=miRNA-1_0.annotations.20090219_annot.csv")


but all I am getting is this message:

...
Warning: probeset <cre-miR1157-star_st> has NumAtoms=4 and NumCells=4
Warning: probeset <cre-miR1162-star_st> has NumAtoms=4 and NumCells=4

Warning: probeset <cre-miR1165-star_st> has NumAtoms=4 and NumCells=4
Warning: probeset <cre-miR1169-star_st> has NumAtoms=4 and NumCells=4
Warning: probeset <mcmv-miR-m01-2-star_st> has NumAtoms=4 and NumCells=4

Warning: probeset <mcmv-miR-m01-3-star_st> has NumAtoms=4 and NumCells=4
Warning: probeset <mcmv-miR-m01-4-star_st> has NumAtoms=4 and NumCells=4
Warning: probeset <mcmv-miR-M23-2-star_st> has NumAtoms=4 and NumCells=4

Warning: probeset <mcmv-miR-m88-1-star_st> has NumAtoms=4 and NumCells=4
Warning: probeset <mcmv-miR-m108-1-star_st> has NumAtoms=4 and NumCells=4
Warning: probeset <mml-miR-1224-star_st> has NumAtoms=4 and NumCells=4

Warning: probeset <hsa-miR-1226-star_st> has NumAtoms=4 and NumCells=4
Warning: probeset <hsa-miR-1228-star_st> has NumAtoms=4 and NumCells=4
Warning: probeset <hsa-miR-664-star_st> has NumAtoms=4 and NumCells=4

Warning: probeset <mdv1-miR-M9-star_st> has NumAtoms=4 and NumCells=4
Warning: probeset <cfa-miR-219-star_st> has NumAtoms=4 and NumCells=4

   <50001> records imported...
   <52900> records imported...Finished
   PM/MM statistics:
      6703 cells with minimum number of PM/MM pairs: 2
      78 cells with maximum number of PM/MM pairs: 47


New dataset <miRNA-1_0_2Xgain> is added to Content...
Importing </home/AYeroslaviz/Jenny_MicroRNA/miRNA-1_0_2Xgain_probe.tab>
as <miRNA-1_0_2Xgain.prb>...
Error: Header column must begin with <Probe Set Name> or <Probe Set ID>

Error: Header line of file <miRNA-1_0_2Xgain_probe.tab> is not correct
...
the file I used here is the *.PSI file from the annotation package of
the affymetrix miRNA-1_0_2Xgain (to be used with FlashTag HSR). I just
rename the end from PSI into tab. I didn't find any other file


Does someone know where I can download the probe data for this array type?*

*
...
Importing </home/AYeroslaviz/Jenny_MicroRNA/miRNA-1_0.annotations.20090219_annot.csv>
as <miRNA-1_0_2Xgain.ann>...
Warning: Number of lines read <7816> is greater than number of genes <7815>


Error: Wrong number of separators in line:
14q-0_st	miRNA_v1	Homo sapiens	Oct 21,
2008	CDBox	=HYPERLINK(http://www-snorna.biotoul.fr/plus.php?id=14q(0)	LINK
to snoRNABase:14q(0))	14q(0)	chr14:100434010-100434086
(+)	77	TGGACCAATGATGAGACAGTGTTTATGAACAAAAGATCATGATTAATCCAGTTCTGCACAAAACACTGAGGTCCATT

Error when reading file <miRNA-1_0.annotations.20090219_annot.csv>.

Apparently the annotation file is also not good enough. Somehow it
count more lines than probes (?).


I used here the annotation file for the newer chip of the miRNA
(2.0),, which is probably the wrong one, but I just wanted to get it
first to work, before I start tweaking with it.

Error in import.expr.scheme("mirna", filedir = getwd(), schemefile =
"miRNA-1_0_2Xgain.CDF",  :


  error in function 'ImportExprSchemes'


I am not exactly sure where I can find the right files for this package.
A Google search found this site: http://microarray.bu.edu/~sshen/xps/, where
complete root files were set to use.

I download the mirna.root file and tried to excute it, but it didn't work
either

I just keep getting the error message:

> mirna.scheme <- root.scheme(rootfile="mirna10.root")
Warning in <TFile::ReadStreamerInfo>: mirna10.root: not a TStreamerInfo object
Warning in <TFile::ReadStreamerInfo>: mirna10.root: not a TStreamerInfo object
Warning in <TFile::ReadStreamerInfo>: mirna10.root: not a TStreamerInfo object
Warning in <TFile::ReadStreamerInfo>: mirna10.root: not a TStreamerInfo object


It will be nice if anyone has already done something like that and can help
me here a little

Thanks
Assa

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