Equivalence between PSDABG and Logarithmic Intensity Error (PLIER) Estimation
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Yang Shi • 0
@ea61ff7a
Last seen 14 days ago
Zheng Zhou

Dear Communities,

There have literatures demonstrated that Human Gene 1.0 ST arrays utilized a methods (PLIER) for accessing reliability for each probe set. I wonder PLIER is quivalent to PSDABG or not. If there is not a equivalence, how to conduct PLIER in R? If PSDABG or DABG could be utilized for calculating PMA matrix, namely assigning p value < 0.04 to 'P', >=0.06 to 'A'. Thanks in advance!

require(oligo)
require(pd.hugene.1.0.st.v1)
affyRaw <- oligo::read.celfiles(celFiles)
eset <- oligo::rma(object = affyRaw)
xpa <- oligo::paCalls(object = affyRaw, method = 'PSDABG')
xpa <- oligo::paCalls(object = affyRaw, method = 'DABG')
pd.hugene.1.0.st.v1 oligo AffymetrixChip • 259 views
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@james-w-macdonald-5106
Last seen 1 day ago
United States

PLIER is a method that Affymetrix developed to summarize probesets. PSDABG and DABG are methods for detecting if a particular probe or probeset is above background. These are not the same thing!

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Thanks for your reply sir! This misunderstanding came from paper indicating "It is not possible, for example, to use either the MAS5 expression summary or detection calling algorithms, since there are no paired mismatch probes; instead Affymetrix provide a new algorithm, probe logarithmic intensity error (plier), and a new method, detection above background (DABG), for assessing the reliability for each probe set". To be honest, my question is how to calculate the PMA matrix of Human Gene 1.0 ST arrays, which do not contain MM probes. I wonder this kinds of arrays could be calcuated by PSDABG and DABG, and then translate into 'P' (p value < 0.04), 'A'(p value >=0.06). Thanks so much sir!

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That's what paCalls is meant for.

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Copy that sir!

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Copy that sir!

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