Hi,
sorry for the wait.
On Fri, Oct 14, 2011 at 6:25 AM, rene.rotterdam
<rene.boettche...@googlemail.com> wrote:
> Hi everyone,
>
> I have a weird situation at the moment, as I am processing my HuEx
> chips according to your suggested script and all columns in the
> fsScores array contain -processed values. I suppose this is not what
> it should look like...
Could you please clarify your question/concern and what you expect instead?
BTW, below you take log2() on a data.frame contain other things that
FIRMA scores, especially the 'unit', 'group' and 'cell' columns. To
preserve those, instead do:
fsScores <- extractDataFrame(fs);
cc <- which(names(fsScores) == "cell");
fsScores[,-(1:cc)] <- log2(fsScores[,-(1:cc)]);
colnames(fsScores) <- gsub("unit", "transcript", colnames(fsScores));
colnames(fsScores) <- gsub("group", "exon", colnames(fsScores));
> head(fsScores)
transcript exon cell S1 S2 S3 S4 S5 S6
1 1 1 1 0.57 1.060 -0.23 -0.67 -0.370 -0.66
2 1 2 2 -0.76 -0.551 -0.26 0.53 0.274 0.33
3 2 1 3 -0.18 -0.682 -1.74 0.24 -0.098 2.07
4 2 2 4 -0.87 2.172 0.63 -1.23 0.407 -0.19
5 2 3 5 0.33 0.034 -0.19 -0.82 0.838 -0.18
6 2 4 6 0.31 0.235 0.84 1.29 -1.718 -0.20
If you add 'addNames=TRUE' to extractDataFrame(), the above gives you:
> head(fsScores)
transcriptName exonName transcript exon cell S1 S2 ...
1 2315251 2315252 1 1 1 0.57 1.060 ...
2 2315251 2315253 1 2 2 -0.76 -0.551 ...
3 2315373 2315374 2 1 3 -0.18 -0.682 ...
4 2315373 2315375 2 2 4 -0.87 2.172 ...
5 2315373 2315376 2 3 5 0.33 0.034 ...
6 2315373 2315377 2 4 6 0.31 0.235 ...
/Henrik
>
> Example:
>
> fsScores[1:8,]
> unit group cell control1
> control2 control3 sample1 sample 2
> 1 0.000000 0.000000 0.000000 -0.41742728 0.561465793
> 0.4043409525 0.007372087 0.3121699
> 2 0.000000 1.000000 1.000000 0.12625074 -0.069064913
> 0.2345612082 0.986910881 0.2556821
> 3 0.000000 1.584963 1.584963 0.37939132 0.818689146
> 0.3518473601 0.482220926 -0.7406933
> 4 0.000000 2.000000 2.000000 0.17216439 0.395573096
> 0.2610864484 -0.100257622 0.2619834
> 5 0.000000 2.321928 2.321928 0.34054436 -1.823549394
> -0.8707103789 -1.531021170 -0.3450005
>
> My code looks like this:
>
> chipType <- "HuEx-1_0-st-v2"
> cdf <- AffymetrixCdfFile$byChipType(chipType,
> tags="fullR3,A20071112,EP")
> cs <- AffymetrixCelSet$byName("all_samples", cdf=cdf)
> setCdf(cs, cdf)
> # BACKGROUND CORRECTION
> bc <- RmaBackgroundCorrection(cs, tag="fullR3")
> csBC <- process(bc,verbose=verbose)
> # QUANTILE NORMALIZATION
> qn <- QuantileNormalization(csBC, typesToUpdate="pm")
> csN <- process(qn, verbose=verbose)
> # FIT SUMMARY MODEL
> plmTr <- ExonRmaPlm(csN, mergeGroups=TRUE)
> fit(plmTr, verbose=verbose)
> cesTr <- getChipEffectSet(plmTr)
> trFit <- extractDataFrame(cesTr, units=NULL, addNames=TRUE)
> # FIRMA
> firma <- FirmaModel(plmTr)
> fit(firma, verbose=verbose)
> fs <- getFirmaScores(firma)
> fsScores <- log2(extractDataFrame(fs))
>
> Any help is greatly appreciated, many thanks in advance.
>
> --
> 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.
>
>
> You received this message because you are subscribed to the Google Groups
> "aroma.affymetrix" group with website http://www.aroma-project.org/.
> To post to this group, send email to aroma-affymetrix@googlegroups.com
> To unsubscribe and other options, go to http://www.aroma-project.org/forum/
>
--
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.
You received this message because you are subscribed to the Google Groups
"aroma.affymetrix" group with website http://www.aroma-project.org/.
To post to this group, send email to aroma-affymetrix@googlegroups.com
To unsubscribe and other options, go to http://www.aroma-project.org/forum/
