Recently, we were questioned [1] about the quality assessment of the raw data which we used in the article “Analysis of Microarray-Identified Genes and MicroRNAs Associated with Idiopathic Pulmonary Fibrosis” published in 14 May 2017 [2]. Aiming at this issue, we asked for the original qualified data of GSE32537 and GSE32538 from the previous authors in Yang’s group [3] and also tested the other samples from GSE53845 and GSE10667. All the qualified control results for GSE32537 (Figure 1(a)–1(c)), GSE32538 (Figure 1(d)), GSE53845 (Table 1), and GSE10667 (Table 2) are listed as follows. No unqualified samples were found.
(a)
(b)
(c) GSE32537
(d) GSE32538
Partek and RLE plot were provided by Yang’s group. There is no unqualified sample in GSE32537 (Figure 1(a)–1(c)) and GSE32538 (Figure 1(a)). Partek software has been cited in over six thousand peer-reviewed articles published in scientific journals such as the prestigious New England Journal of Medicine, Cell, and Nature [4, 5]. Topics include drug research, human genetics, and disease relationships, causes, diagnosis, and treatments (http://www.partek.com/publications). Also, it is recommended by the NIH (https://ostr.cancer.gov/btep/software/partek).
According to the samples from GSE10667 (Table 1) and GSE53845 (Table 2), because the data are obtained in the Agilent chip platform, they can be qualified using CV and check ratio (http://www.chem.agilent.com/cag/bsp/products/1color/OnecolorPerformanceposter_finaldraft.pdf), and we found no unqualified samples.
Conflicts of Interest
The authors declare that they have no conflicts of interest.
Acknowledgments
This work was funded by the National Natural Science Foundation of China (81600043, 81570053, and 09411951600) and Shanghai Municipal Natural Science Foundation (16ZR1432100).