Hi,
I'm new here, and I'm sorry if I'll post obvious questions. I looked
throughout the newsgroup and on the aroma.affymetrix web page, but I
couldn't find the answer from my question, so here it is:
I'm trying to analyze a 950 chip dataset from Wooster et al (318
cancer cell lines in triplicate - on average). So I followed the steps
as in the web page, and arrived to the plotNuse and plotRle part.
Nothing wrong so far, and I can clearly see that some arrays are
outliers and possibly have poor quality, so I would like to remove
them for further analyses. The issue is, I don't have a clue how to
know which ones they are and how to remove them, because the plots are
too crowdy and I don't know how to see what is what and how to take it
out.
Some information:
sessionInfo()
R version 2.10.1 (2009-12-14)
i386-pc-mingw32
locale:
[1] LC_COLLATE=English_United States.1252
[2] LC_CTYPE=English_United States.1252
[3] LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C
[5] LC_TIME=English_United States.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods
base
other attached packages:
[1] aroma.affymetrix_1.5.0 aroma.apd_0.1.7
affxparser_1.18.0
[4] R.huge_0.2.0 aroma.core_1.5.0
aroma.light_1.16.0
[7] matrixStats_0.2.1 R.rsp_0.3.6
R.cache_0.3.0
[10] R.filesets_0.8.1 digest_0.4.2
R.utils_1.4.0
[13] R.oo_1.7.2 R.methodsS3_1.2.0
loaded via a namespace (and not attached):
[1] tools_2.10.1
About my data:
> print(qam)
QualityAssessmentModel:
Name: Dataset Wooster
Tags: RBC,QN,RMA,QC
Path: qcData/Dataset Wooster,RBC,QN,RMA,QC/HG-U133_Plus_2
Chip-effect set:
ChipEffectSet:
Name: Dataset Wooster
Tags: RBC,QN,RMA
Path: plmData/Dataset Wooster,RBC,QN,RMA/HG-U133_Plus_2
Platform: Affymetrix
Chip type: HG-U133_Plus_2,monocell
Number of arrays: 950
Names: 1A2 _SS392785_HG-U133_Plus_2_HCHP-186915_, 1A2 _SS392786_HG-
U133_Plus_2_HCHP-186916_, ..., YAPC_SS331347_HG-
U133_Plus_2_HCHP-182915_
Time period: [not reported if more than 500 arrays]
Total file size: 546.67MB
RAM: 0.84MB
Parameters: (probeModel: chr "pm")
RAM: 0.00MB
And a final question (a very stupid one, I'm sure): once I finished my
quality controls, how do I average technical replicates?
Thank you and I beg your pardon for any silly question
Gabriele
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