Question: (Closed) Any way to verify the quality and accuracy of preprocessed Affymetrix microarray expression data?
0
gravatar for Jurat Shahidin
17 months ago by
Chicago, IL, USA
Jurat Shahidin80 wrote:

I have preprocessed Affymetrix microarrays expression data matrix (Affymetrix probe-sets in rows (32830 probesets), and RNA samples in columns (735 samples)) as follows:

HTA20_rma <- load("HTA20_RMA.RData")

> eset_HTA20[1:10,1:3]
             Tarca_001_P1A01 Tarca_003_P1A03 Tarca_004_P1A04
1_at                6.062215        6.125023        5.875502
10_at               3.796484        3.805305        3.450245
100_at              5.849338        6.191562        6.550525
1000_at             3.567779        3.452524        3.316134
10000_at            6.166815        5.678373        6.185059
100009613_at        4.443027        4.773199        4.393488
100009676_at        5.836522        6.143398        5.898364
10001_at            6.330018        5.601745        6.137984
10002_at            4.922339        4.711765        4.628124
10003_at            2.689344        2.771010        2.556756

since I am not able to access raw cell files at the moment, I am experimenting eset_HTA20 Affymetrix expression data for my downstream analysis. However, I am interested to verify the quality and accuracy of this preprocessed eset_HTA20 data once again. To do so, I believe using limma' function such as plotDensities:

## generate plotDensities graph for each sample (a.k.a, RNA sample)
eset_bc <- backgroundCorrect(eset_HTA20, method = "normexp")
plotDensities(eset_bc)

and I got following densities plot which is not intuitive to me to understand:

meanwhile, when I tried to normalize expression data, I got this error:

> eset_MA <- normalizeWithinArrays(eset_bc)
Error: $ operator is invalid for atomic vectors
plotDensities(eset_MA)

Is there any way that I can verify the quality and accuracy of this preprocessed Affymetrix expression data in R? How can I lay out a concrete evaluation procedure for normalization and background correction on this data? Instead of generating densities plot, what else I can do about it? How can I make density plot more meaningful for downstream analysis? Any idea?

ADD COMMENTlink modified 17 months ago • written 17 months ago by Jurat Shahidin80

In future, if you post somewhere else, then please make us aware so that we do not waste our efforts in responding. You posted on Bioconductor and it has been answered already by the leading figure (in the World) in microarray analyses: https://support.bioconductor.org/p/122063/

This thread will be closed.

ADD REPLYlink written 17 months ago by Kevin Blighe68k

agreed. I will follow the community rule. Thanks for your help

ADD REPLYlink written 17 months ago by Jurat Shahidin80
1

Sure thing - no problem. It was great that Gordon and James responded to you on Bioconductor. Cannot think of better people :)

ADD REPLYlink modified 17 months ago • written 17 months ago by Kevin Blighe68k
1

will learn more from your answer on biostar, thanks again for helping me out.

ADD REPLYlink written 17 months ago by Jurat Shahidin80
Please log in to add an answer.
The thread is closed. No new answers may be added.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 2248 users visited in the last hour