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