Entering edit mode
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')
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!
That's what
paCallsis meant for.Copy that sir!
Copy that sir!