[BioC] Low-level analysis of custom microarrays

[Teresa Colombo]

Hi Dear BioC list,

I am a newbie and apologize in advance if this is just a stupid
question. But I've been trapped by this problem since 2 weeks now and
dunno how to move on from here without a little help...

my TASK: Perform background correction on (miRNA) microarray data from
a custom chip, taking into account slide spatial info (no simple
subtraction of background intensities).

my INPUT DATA FORMAT: For each slide, a tab delimited text file
carrying the following info:
"Probe_ID"      "Row"   "Column"        "Density_mean_{A}"
"Density_st.dev._ {A}"

For example, the following are the first 5 lines for one of the slides:
"empty" 1       1       174,2   8,57
"hsa-let-7a"    1       2       49522,89        343,1
"hsa-miR-150"   1       3       40738,46        677,54
"hsa-miR-204"   1       4       209,61  15,48
"hsa-miR-32"    1       5       223,07  15,24

There are 7 replicates for each experimental probe + many internal
control probes (row.names are not unique).

my QUESTION:
Is there any R package/function available to perform background
correction taking into account the slide design/spatial info (amenable
to be used with this kind of raw input data - e.g., neither .CEL nor
Illumina input data)?

my R version - attached packages:
> sessionInfo()
R version 2.4.0 Patched (2006-11-25 r39997)
i486-pc-linux-gnu

locale:
LC_CTYPE=it_IT at euro;LC_NUMERIC=C;LC_TIME=it_IT at euro;LC_COLLATE=it_IT at euro;LC_MONETARY=it_IT at euro;LC_MESSAGES=it_IT at euro;LC_PAPER=it_IT at euro;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=it_IT at euro;LC_IDENTIFICATION=C

attached base packages:
[1] "tools"     "stats"     "graphics"  "grDevices" "utils"     "datasets"
[7] "methods"   "base"

other attached packages:
    affy   affyio  Biobase
"1.12.2"  "1.2.0" "1.12.2"


Thank you in advance for your help and time!

Best,
teresa