Question: Some questions about chip quality control
gravatar for llkxiaolan
15 months ago by
llkxiaolan0 wrote:

When I look at the literature on chip analysis, I've seen many articles that first analyze the quality of the chip. I would like to ask what standards can be used for chip quality analysis? 

I know there are scaling factors, β-actin and GAPDH, percent present,NUSE box chart and RLE box chart .

But there have specific standards for the NUSE line drawings and the RLE box drawings, for example -0.25<RLE<0.25 and 1-0.2<NUSE<1+0.2 ?

ADD COMMENTlink modified 15 months ago by Guido Hooiveld2.3k • written 15 months ago by llkxiaolan0
gravatar for Guido Hooiveld
15 months ago by
Guido Hooiveld2.3k
Wageningen University, Wageningen, the Netherlands
Guido Hooiveld2.3k wrote:

In practice we almost never look at the values of these metrics as such, but rather look for samples that deviate from the majority. We then check whether e.g. pseudo-images indicate the presence of stains, or that some samples e.g. belong to a different tissue (e.g. liver versus intestine). In case of the later deviations are very likely because of a 'biological' reason.

Regarding the NUSE box plots; for us this is the most sensitive QC parameter, and we use as rule of thumb that a sample passes that parameter if the corresponding 'box' (i.e. first and third quartiles) still 'touches' the 1.00 line. If that's not the case, we check the other QC parameters and sample source if there is a technical problem or not.


I found these papers very informative regarding interpretation of the various QC metrics:

Brettschneider et al. Quality Assessment for Short Oligonucleotide Microarray Data. Technometrics, 2008;50:3, 241-264. DOI.

Heber & Sick. Quality assessment of Affymetrix GeneChip data. OMICS. 2006;10(3):358-68. DOI.

McCall et al. Assessing affymetrix GeneChip microarray quality. BMC Bioinformatics. 2011;12:137. DOI.

Rosikiewicz & Robinson-Rechavi. IQRray, a new method for Affymetrix microarray quality control, and the homologous organ conservation score, a new benchmark method for quality control metrics. Bioinformatics. 2014;30(10):1392-9. DOI.



ADD COMMENTlink modified 15 months ago • written 15 months ago by Guido Hooiveld2.3k

Thank you very much. I'll read these articles carefully 

ADD REPLYlink written 15 months ago by llkxiaolan0
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