[BioC] limma and marray data import problem

Piotr Stępniak piotrek.stepniak at gmail.com
Sat May 31 12:55:25 CEST 2008

Hello Everyone,

I am Piotr Stępniak, B.Sc. in Biotechnology, currently under M.Sc.
course at Adam Mickiewicz University in Poznań, Poland. I am working
in Polish Science Academy in microarray experiments group.

I'm a newbie in R and BioC, so please forgive me if my question is easy...

I'm having problem with data import to RGList or marrayRaw objects.
Using the following instruction:
bialkoRaw<- read.maimages( dir(pattern="gpr"), columns=list(G="F543
Median", Gb="B543 Median", R="F633 Median", Rb="B633 Median"),
annotation=c("Block", "Column", "Row", "Name", "ID"), row.names=NULL)
The data seems to load, but $genes table looks odd, I guess the column
names are shifted right by 1 column:
  Block Column         Row Name   ID
1     1      1  ERG_Operon 2078 2647
2     2      1  ERG_Operon 2078 3102
3     3      1  ERG_Operon 2078 3549
4     4      1 FLT3_Operon 2322 3994
5     5      1 FLT3_Operon 2322 4444
2635 more rows ...
This I think causes printer layout to be imported wrongly and then any
other try to process the data (e.g. quality tests) produce such error
 Error in if (is.int(totalPlate)) { : argument is of length zero

The data is obtained with ScanArrayExpress software, so I have it in
gpr or csv files, both give similar errors, but loading csv files
seems also to fail import values for each channel and gets only the
file name headers.

Marray import also fails, I will skip the info about it not to enlarge
the mail unnecessarily.

My R session info is as follows:
> sessionInfo()
R version 2.6.2 (2008-02-08)


attached base packages:
 [1] grid      splines   tools     stats     graphics  grDevices utils
 [8] datasets  methods   base

other attached packages:
 [1] arrayQuality_1.18.0  gridBase_0.4-3       hexbin_1.14.0
 [4] convert_1.16.0       RColorBrewer_1.0-2   cluster_1.11.10
 [7] arrayMagic_1.16.1    genefilter_1.16.0    survival_2.34-1
[10] marray_1.18.0        vsn_3.6.0            limma_2.14.1
[13] affy_1.16.0          preprocessCore_1.0.0 affyio_1.8.0
[16] Biobase_1.16.3       lattice_0.17-7

loaded via a namespace (and not attached):
[1] AnnotationDbi_1.0.6 DBI_0.2-4           RSQLite_0.6-8
[4] annotate_1.18.0     rcompgen_0.1-17

I think I should also say that these data causes import problems to
any other data analysis software :( I also tried to read the printer
layout from gal file, but all I got was "Block, Row, Column, ID
columns not found" error.

I'd greatly appreciate any help, please.

Yours faithfully,
Piotr Stępniak

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