Limits...
PreP+07: improvements of a user friendly tool to preprocess and analyse microarray data.

Martin-Requena V, Muñoz-Merida A, Claros MG, Trelles O - BMC Bioinformatics (2009)

Bottom Line: PreP+07 implementation provides a high degree of freedom in selecting and organizing a small set of widely used data processing protocols, and can handle many data formats.Its reliability has been proven so that a laboratory researcher can afford a statistical pre-processing of his/her microarray results and obtain a list of differentially expressed genes using PreP+07 without any programming skills.All of this gives support to scientists that have been using previous PreP releases since its first version in 2003.

View Article: PubMed Central - HTML - PubMed

Affiliation: Computer Architecture Department, University of Málaga, Málaga, Spain. vickymr@ac.uma.es

ABSTRACT

Background: Nowadays, microarray gene expression analysis is a widely used technology that scientists handle but whose final interpretation usually requires the participation of a specialist. The need for this participation is due to the requirement of some background in statistics that most users lack or have a very vague notion of. Moreover, programming skills could also be essential to analyse these data. An interactive, easy to use application seems therefore necessary to help researchers to extract full information from data and analyse them in a simple, powerful and confident way.

Results: PreP+07 is a standalone Windows XP application that presents a friendly interface for spot filtration, inter- and intra-slide normalization, duplicate resolution, dye-swapping, error removal and statistical analyses. Additionally, it contains two unique implementation of the procedures - double scan and Supervised Lowess-, a complete set of graphical representations - MA plot, RG plot, QQ plot, PP plot, PN plot - and can deal with many data formats, such as tabulated text, GenePix GPR and ArrayPRO. PreP+07 performance has been compared with the equivalent functions in Bioconductor using a tomato chip with 13056 spots. The number of differentially expressed genes considering p-values coming from the PreP+07 and Bioconductor Limma packages were statistically identical when the data set was only normalized; however, a slight variability was appreciated when the data was both normalized and scaled.

Conclusion: PreP+07 implementation provides a high degree of freedom in selecting and organizing a small set of widely used data processing protocols, and can handle many data formats. Its reliability has been proven so that a laboratory researcher can afford a statistical pre-processing of his/her microarray results and obtain a list of differentially expressed genes using PreP+07 without any programming skills. All of this gives support to scientists that have been using previous PreP releases since its first version in 2003.

Show MeSH

Related in: MedlinePlus

Double-Scan procedure. In (1) the transfer function of the photo detectors used in the scanners is depicted. At high intensities the relationship between the incident light level and the output current begins to deviate from the ideal intensity in an effect called saturation that is typically drawn in an arrow shape (see 2a). On the other hand, quantization occurs when digitizing. All the unlimited physical values have to be encoded by a reduced set of discrete values, producing the same rate for a range of different values [21]. This effect can be observed in (2b) as a set of parallel lines. 2-Scan strategy [16] is based on the rather simple idea of producing two images with different calibrations, from which a mathematical model produces a coherent but extended range of values.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC2657788&req=5

Figure 2: Double-Scan procedure. In (1) the transfer function of the photo detectors used in the scanners is depicted. At high intensities the relationship between the incident light level and the output current begins to deviate from the ideal intensity in an effect called saturation that is typically drawn in an arrow shape (see 2a). On the other hand, quantization occurs when digitizing. All the unlimited physical values have to be encoded by a reduced set of discrete values, producing the same rate for a range of different values [21]. This effect can be observed in (2b) as a set of parallel lines. 2-Scan strategy [16] is based on the rather simple idea of producing two images with different calibrations, from which a mathematical model produces a coherent but extended range of values.

Mentions: Double scan implementation is based on a robust mathematical model described in [18] and requires the identification of the saturation model (clipper or gamma). Adjustments can be visualized with the 'intensity-intensity' plot. It shows the spots according to the intensity measured in a low sensitivity scan and a high sensitivity scan for both the green and red channels. This plot can also be used for the comparison of two replicated slides or scans. If the replication is properly done, the spots must show a linear relation; otherwise, when the scans have different calibrations, the data will follow a non linear curve due to saturation or calibration effects (see Figure 2).


PreP+07: improvements of a user friendly tool to preprocess and analyse microarray data.

Martin-Requena V, Muñoz-Merida A, Claros MG, Trelles O - BMC Bioinformatics (2009)

Double-Scan procedure. In (1) the transfer function of the photo detectors used in the scanners is depicted. At high intensities the relationship between the incident light level and the output current begins to deviate from the ideal intensity in an effect called saturation that is typically drawn in an arrow shape (see 2a). On the other hand, quantization occurs when digitizing. All the unlimited physical values have to be encoded by a reduced set of discrete values, producing the same rate for a range of different values [21]. This effect can be observed in (2b) as a set of parallel lines. 2-Scan strategy [16] is based on the rather simple idea of producing two images with different calibrations, from which a mathematical model produces a coherent but extended range of values.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2657788&req=5

Figure 2: Double-Scan procedure. In (1) the transfer function of the photo detectors used in the scanners is depicted. At high intensities the relationship between the incident light level and the output current begins to deviate from the ideal intensity in an effect called saturation that is typically drawn in an arrow shape (see 2a). On the other hand, quantization occurs when digitizing. All the unlimited physical values have to be encoded by a reduced set of discrete values, producing the same rate for a range of different values [21]. This effect can be observed in (2b) as a set of parallel lines. 2-Scan strategy [16] is based on the rather simple idea of producing two images with different calibrations, from which a mathematical model produces a coherent but extended range of values.
Mentions: Double scan implementation is based on a robust mathematical model described in [18] and requires the identification of the saturation model (clipper or gamma). Adjustments can be visualized with the 'intensity-intensity' plot. It shows the spots according to the intensity measured in a low sensitivity scan and a high sensitivity scan for both the green and red channels. This plot can also be used for the comparison of two replicated slides or scans. If the replication is properly done, the spots must show a linear relation; otherwise, when the scans have different calibrations, the data will follow a non linear curve due to saturation or calibration effects (see Figure 2).

Bottom Line: PreP+07 implementation provides a high degree of freedom in selecting and organizing a small set of widely used data processing protocols, and can handle many data formats.Its reliability has been proven so that a laboratory researcher can afford a statistical pre-processing of his/her microarray results and obtain a list of differentially expressed genes using PreP+07 without any programming skills.All of this gives support to scientists that have been using previous PreP releases since its first version in 2003.

View Article: PubMed Central - HTML - PubMed

Affiliation: Computer Architecture Department, University of Málaga, Málaga, Spain. vickymr@ac.uma.es

ABSTRACT

Background: Nowadays, microarray gene expression analysis is a widely used technology that scientists handle but whose final interpretation usually requires the participation of a specialist. The need for this participation is due to the requirement of some background in statistics that most users lack or have a very vague notion of. Moreover, programming skills could also be essential to analyse these data. An interactive, easy to use application seems therefore necessary to help researchers to extract full information from data and analyse them in a simple, powerful and confident way.

Results: PreP+07 is a standalone Windows XP application that presents a friendly interface for spot filtration, inter- and intra-slide normalization, duplicate resolution, dye-swapping, error removal and statistical analyses. Additionally, it contains two unique implementation of the procedures - double scan and Supervised Lowess-, a complete set of graphical representations - MA plot, RG plot, QQ plot, PP plot, PN plot - and can deal with many data formats, such as tabulated text, GenePix GPR and ArrayPRO. PreP+07 performance has been compared with the equivalent functions in Bioconductor using a tomato chip with 13056 spots. The number of differentially expressed genes considering p-values coming from the PreP+07 and Bioconductor Limma packages were statistically identical when the data set was only normalized; however, a slight variability was appreciated when the data was both normalized and scaled.

Conclusion: PreP+07 implementation provides a high degree of freedom in selecting and organizing a small set of widely used data processing protocols, and can handle many data formats. Its reliability has been proven so that a laboratory researcher can afford a statistical pre-processing of his/her microarray results and obtain a list of differentially expressed genes using PreP+07 without any programming skills. All of this gives support to scientists that have been using previous PreP releases since its first version in 2003.

Show MeSH
Related in: MedlinePlus