Hi Anbarasu.
To extract just the raw probe intensities (before BG adjustment or
normalization), how about something like:
cdf <- AffymetrixCdfFile$byChipType(chipType, tags="coreR3,A20071112,EP")
cs <- AffymetrixCelSet$byName("tissues", cdf=cdf)
u <- 1:nbrOfUnits(cdf)
u <- 1:10 # could use line above, but use subset to make it quick
ugcM <- getUnitGroupCellMap(cdf, units=u, retNames=TRUE)
d <- extractMatrix(cs, cells=ugcM$cell)
rownames(d) <- paste(ugcM$unit, ugcM$group, sep=".")
There are of course other possibilities for the rownames if you chose, but here
is what it would give:
> rownames(d) <- paste(ugcM$unit, ugcM$group, sep=".")
> head(d)
huex_wta_spleen_A huex_wta_spleen_B huex_wta_spleen_C
2315251.2315252 49 46 30
2315251.2315252 41 48 37
2315251.2315252 68 46 40
2315251.2315252 46 39 32
2315251.2315253 34 26 31
2315251.2315253 30 30 28
huex_wta_testes_A huex_wta_testes_B huex_wta_testes_C
2315251.2315252 131 111 156
2315251.2315252 96 81 153
2315251.2315252 138 102 146
2315251.2315252 72 49 56
2315251.2315253 45 33 48
2315251.2315253 30 39 31
huex_wta_thyroid_A huex_wta_thyroid_B huex_wta_thyroid_C
2315251.2315252 31 57 70
2315251.2315252 49 40 63
2315251.2315252 33 54 61
2315251.2315252 30 53 46
2315251.2315253 29 53 35
2315251.2315253 26 38 39
Hope that helps.
Mark
On 2011-02-09, at 3:38 AM, Anbarasu L A wrote:
> Hi All,
>
> I have been looking at extracting raw data for core transcripts from
> HuEx-1_0-st-v2 chip type. I have downloaded the custom CDF file provided in
> http://www.aroma-project.org/node/122.
>
> chipType <- "HuEx-1_0-st-v2"
> cdf <- AffymetrixCdfFile$byChipType(chipType, tags="core")
> print(cdf)
> AffymetrixCdfFile:
> Path: annotationData/chipTypes/HuEx-1_0-st-v2
> Filename: HuEx-1_0-st-v2,core.cdf
> Filesize: 32.00MB
> Chip type: HuEx-1_0-st-v2,core
> RAM: 0.00MB
> File format: v4 (binary; XDA)
> Dimension: 2560x2560
> Number of cells: 6553600
> Number of units: 22010
> Cells per unit: 297.76
> Number of QC units: 0
>
> How can I access these 22010 units (transcripts) and extract un normalized
> intensity values? If I use: getCellIndices(cdf, unlist=TRUE, useNames=FALSE),
> I am getting intensity data for 893395 probes.
>
> Thanks in advance.
>
> Best regards,
> Anbarasu
>
>
>
>
>
> --
> When reporting problems on aroma.affymetrix, make sure 1) to run the latest
> version of the package, 2) to report the output of sessionInfo() and
> traceback(), and 3) to post a complete code example.
>
>
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------------------------------
Mark Robinson, PhD (Melb)
Epigenetics Laboratory, Garvan
Bioinformatics Division, WEHI
e: mrobin...@wehi.edu.au
e: m.robin...@garvan.org.au
p: +61 (0)3 9345 2628
f: +61 (0)3 9347 0852
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version of the package, 2) to report the output of sessionInfo() and
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