| Title: | Affymetrix Spike-in Langmuir Isotherm Data Analysis Tool |
|---|---|
| Description: | SpikeLI is a package that performs the analysis of the Affymetrix spike-in data using the Langmuir Isotherm. The aim of this package is to show the advantages of a physical-chemistry based analysis of the Affymetrix microarray data compared to the traditional methods. The spike-in (or Latin square) data for the HGU95 and HGU133 chipsets have been downloaded from the Affymetrix web site. The model used in the spikeLI package is described in details in E. Carlon and T. Heim, Physica A 362, 433 (2006). |
| Authors: | Delphine Baillon, Paul Leclercq <[email protected]>, Sarah Ternisien, Thomas Heim, Enrico Carlon <[email protected]> |
| Maintainer: | Enrico Carlon <[email protected]> |
| License: | GPL-2 |
| Version: | 2.65.0 |
| Built: | 2024-07-25 04:42:54 UTC |
| Source: | https://github.com/bioc/spikeLI |
spikeLI performs a series of analysis of Affymetrix spike-in data using inputs from physical-chemistry. It illustrates the advantages of such approach in determining expression levels and in identifying outliers compared to other methods. The analysis so far is restricted to spike-in genes. It will be extended to a generic CEL file. spikeLI does not require affy (and it is independent of any other bioconductor packages) as it reads spike-in data from a data frame variable hgu which is contained in the package.
| Package: | spikeLI |
| Type: | Package |
| Version: | 1.0 |
| Date: | 2006-05-05 |
| License: | GNU Public License |
The package contains three basic functions: - Ivsc plot intensities as function of spike-in concentration for a fixed probe. - IvsDG plot intensities as function of affinity for a given probe set at fixed concentration. - collapse plot of intensities both as a function of concentration and affinities.
Delphine Baillon, Paul Leclercq, Sarah Ternisien, Thomas Heim and Enrico Carlon
Maintainer: Enrico Carlon <[email protected]>
E. Carlon and T. Heim, Physica A 362, 433 (2006).
collapse, Ivsc, IvsDG, hgu, SPIKE_IN, SPIKE_INA, SPIKE_INB, SPIKE_INH
, SPIKE_IN95
This function takes as input one or more (up to four) probe sets of the Latin square spike-in data and produces collapse plots. A collapse plot contains data of different concentrations into a single graph. The user can compare in how far the data follows the predicted Langmuir behavior which is also given in the plot. Two models are compared: the basic Langmuir Isotherm and the Langmuir Isotherm with hybridization in solution.
collapse(probe_set, param = "NULL", probes = "NULL", output = "NULL", filename = "NULL")collapse(probe_set, param = "NULL", probes = "NULL", output = "NULL", filename = "NULL")
probe_set |
This has to take the value of a probe set |
param |
In input one or more probe sets can be given |
probes |
A vector containing the probes |
output |
"PS" output on a postscript file |
filename |
the file in which collapses are given |
Delphine Baillon, Paul Leclercq, Sarah Ternisien, Thomas Heim and Enrico Carlon
E. Carlon and T. Heim, Physica A 362, 433 (2006).
Ivsc, IvsDG, hgu, SPIKE_IN, SPIKE_INA, SPIKE_INB, SPIKE_INH
## You may display the matched intensities of a Probe-Set according to the Delta-G value collapse("1091_at") ## You may restrict the value to the Perfect match or mis-matches collapse("1091_at","PM") ## You may restrict the values risplayed for only a number of probes collapse("1091_at",probes=c(1,9)) ## You may output the graphs to a postscript file collapse("1091_at",output="PS",filename="outfile.ps") ## You may display up to 4 probe-sets in the same window collapse(c("1091_at","37777_at",SPIKE_INA[1:2])) ## You can also use the values of the probe-sets contained in one of the Vectors of Human, Bacteria, ## or Artificial Probe-sets collapse(SPIKE_INH)## You may display the matched intensities of a Probe-Set according to the Delta-G value collapse("1091_at") ## You may restrict the value to the Perfect match or mis-matches collapse("1091_at","PM") ## You may restrict the values risplayed for only a number of probes collapse("1091_at",probes=c(1,9)) ## You may output the graphs to a postscript file collapse("1091_at",output="PS",filename="outfile.ps") ## You may display up to 4 probe-sets in the same window collapse(c("1091_at","37777_at",SPIKE_INA[1:2])) ## You can also use the values of the probe-sets contained in one of the Vectors of Human, Bacteria, ## or Artificial Probe-sets collapse(SPIKE_INH)
This datasets contains the values of the latine square matrix for the hgu133 Affymetrix Microarrays
data(conc133)data(conc133)
The format is: num [1:14] 0 0.125 0.25 0.5 1 2 4 8 16 32 ...
Ivsc, IvsDG, collapse, SPIKE_IN, SPIKE_INA, SPIKE_INB, SPIKE_INH
data(conc133)data(conc133)
This datasets contains the values of the latine square matrix for the hgu95 Affymetrix Microarrays
data(conc95)data(conc95)
The format is: num [1:14] 0 0.25 0.5 1 2 4 8 16 32 64 ...
Ivsc, IvsDG, collapse, SPIKE_IN, SPIKE_INA, SPIKE_INB, SPIKE_INH
data(conc95)data(conc95)
This selected probe sets information contains the sequence of the selected probe sets, as well as the match and mismatch onformation and Delta G value required for the langmuir analysis
data(hgu)data(hgu)
A data frame with 11452 observations on the following 9 variables.
Probe.Set.NameName of probe set
conca numeric vector
Ipma numeric vector
Imma numeric vector
SeqDNA Sequence of the probe
DGpmDG value of perfect match of the probe
DGmmDelta G value of the mismatch of the probe
DGRNADelta G value of the RNA
FILEa factor with levels HGU133 HGU95
E. Carlon and T. Heim, Physica A 362, 433 (2006).
Ivsc, IvsDG, collapse, SPIKE_IN, SPIKE_INA, SPIKE_INB, SPIKE_INH
data(hgu) ## maybe str(hgu) ; plot(hgu) ...data(hgu) ## maybe str(hgu) ; plot(hgu) ...
The function Ivsc plots intensity as a function of a concentration for a given probe in the spike-in Latin square experiments. It also peforms a non-linear data fit (using the package nls in the R-package stats) of the experimental data using the Langmuir Isotherm: I = I0 + Ac/(K+c) Solid and dashed lines are best fits according to this formula. Imax in the plot are given by Imax=I0+A, ie the asymptotic intensity in the limit of c to infinity.
Ivsc(probe_set, probe = "NULL", outfile = "NULL")Ivsc(probe_set, probe = "NULL", outfile = "NULL")
probe_set |
Probe set number of the probe set analyzed |
probe |
Integer giving the probe number (if not give the probe 1 is selected) |
outfile |
output the plotted data to a postscript file |
Some probes have an irregular behavior and the non-linear square fit does not converge.
Delphine Baillon, Paul Leclercq, Sarah Ternisien, Thomas Heim and Enrico Carlon
Maintainer: Enrico Carlon <[email protected]>
E. Carlon and T. Heim, Physica A 362, 433 (2006).
collapse, IvsDG, hgu, SPIKE_IN, SPIKE_INA, SPIKE_INB, SPIKE_INH
Ivsc("37777_at",4)Ivsc("37777_at",4)
IvsDG plots intensity vs affinity (or free energy) for a probe set at a given concentration. The outcome is compared with the prediction from the Langmuir isotherm at that concentration. Two graphs are shown: on the left intensity vs. probe number for PM (blue) and MM (red); on the right the same value plotted as function of the affinities. The black line is the Langmuir Isotherm at the given concentration. The two green lines correspond to concentrations fourfold higher and lower compared to the given one.
IvsDG(probe_set, conc, outfile = "NULL")IvsDG(probe_set, conc, outfile = "NULL")
probe_set |
Probe set number of the probe set analyzed |
conc |
Concentration value |
outfile |
"PS" output on a postscript file |
Delphine Baillon, Paul Leclercq, Sarah Ternisien, Thomas Heim and Enrico Carlon
Maintainer: Enrico Carlon <[email protected]>
E. Carlon and T. Heim, Physica A 362, 433 (2006).
Ivsc, collapse, hgu, SPIKE_IN, SPIKE_INA, SPIKE_INB, SPIKE_INH
data(hgu) IvsDG("1024_at",64)data(hgu) IvsDG("1024_at",64)
This dataset contains the names of the Probe-Sets contained in the HGU dataset
data(SPIKE_IN)data(SPIKE_IN)
A string containing the name of the genes
E. Carlon and T. Heim, Physica A 362, 433 (2006).
Ivsc, IvsDG, collapse, hgu, SPIKE_INA
, SPIKE_INB, SPIKE_INH, SPIKE_IN95
## you can first check if the data matches the predicted hybridisation value according to the langmuir ## value, from the intensity versus the concentration value Ivsc(SPIKE_IN[3]) ## you can then plot the value of the Intensity of the probe with the predicted value of the hybridisation ## according to the Delta G, value IvsDG(SPIKE_IN[5],64) ## The collapse function will finally plot all the values of the probe set according to ## the langmuir absorption theory collapse(SPIKE_IN[2]) ## By comparing the matched value and the mismatches, you will be able to identify errors which ## could have done while sampling the data, or if the error happens repeatedly this will show errors ## which will have happened while sequencing old data.## you can first check if the data matches the predicted hybridisation value according to the langmuir ## value, from the intensity versus the concentration value Ivsc(SPIKE_IN[3]) ## you can then plot the value of the Intensity of the probe with the predicted value of the hybridisation ## according to the Delta G, value IvsDG(SPIKE_IN[5],64) ## The collapse function will finally plot all the values of the probe set according to ## the langmuir absorption theory collapse(SPIKE_IN[2]) ## By comparing the matched value and the mismatches, you will be able to identify errors which ## could have done while sampling the data, or if the error happens repeatedly this will show errors ## which will have happened while sequencing old data.
This dataset contains a set of gene names contained in the HGU95 dataset
data(SPIKE_IN95)data(SPIKE_IN95)
The set of spike-in gene names contained in the HGU dataset
This data is experimental data extracted from the publicly available HGU dataset
E. Carlon and T. Heim, Physica A 362, 433 (2006).
Ivsc, IvsDG, collapse, SPIKE_IN, hgu
, SPIKE_INA, SPIKE_INB, SPIKE_INH
## you can first check if the data matches the predicted hybridisation value according to the langmuir ## value, from the intensity versus the concentration value Ivsc(SPIKE_IN95[1]) ## you can then plot the value of the Intensity of the probe with the predicted value of the hybridisation ## according to the Delta G, value IvsDG(SPIKE_IN95[4],128) ## The collapse function will finally plot all the values of the probe set according to ## the langmuir absorption theory collapse(SPIKE_IN95[2]) ## By comparing the matched value and the mismatches, you will be able to identify errors which ## could have done while sampling the data, or if the error happens repeatedly this will show errors ## which will have happened while sequencing old data.## you can first check if the data matches the predicted hybridisation value according to the langmuir ## value, from the intensity versus the concentration value Ivsc(SPIKE_IN95[1]) ## you can then plot the value of the Intensity of the probe with the predicted value of the hybridisation ## according to the Delta G, value IvsDG(SPIKE_IN95[4],128) ## The collapse function will finally plot all the values of the probe set according to ## the langmuir absorption theory collapse(SPIKE_IN95[2]) ## By comparing the matched value and the mismatches, you will be able to identify errors which ## could have done while sampling the data, or if the error happens repeatedly this will show errors ## which will have happened while sequencing old data.
This dataset contains the names of the probesets contained in the hgu dataset
data(SPIKE_INA)data(SPIKE_INA)
This dataset contains a set of String containing the names of the Artificial genes contained in the HGU dataset
E. Carlon and T. Heim, Physica A 362, 433 (2006).
Ivsc, IvsDG, collapse, SPIKE_IN, hgu
, SPIKE_INB, SPIKE_INH
## you can first check if the data matches the predicted hybridisation value according to the langmuir ## value, from the intensity versus the concentration value Ivsc(SPIKE_INA[1]) ## you can then plot the value of the Intensity of the probe with the predicted value of the hybridisation ## according to the Delta G, value IvsDG(SPIKE_INA[4],128) ## The collapse function will finally plot all the values of the probe set according to ## the langmuir absorption theory collapse(SPIKE_INA[2]) ## By comparing the matched value and the mismatches, you will be able to identify errors which ## could have done while sampling the data, or if the error happens repeatedly this will show errors ## which will have happened while sequencing old data.## you can first check if the data matches the predicted hybridisation value according to the langmuir ## value, from the intensity versus the concentration value Ivsc(SPIKE_INA[1]) ## you can then plot the value of the Intensity of the probe with the predicted value of the hybridisation ## according to the Delta G, value IvsDG(SPIKE_INA[4],128) ## The collapse function will finally plot all the values of the probe set according to ## the langmuir absorption theory collapse(SPIKE_INA[2]) ## By comparing the matched value and the mismatches, you will be able to identify errors which ## could have done while sampling the data, or if the error happens repeatedly this will show errors ## which will have happened while sequencing old data.
This dataset contains the names of the Bacteria probe-sets contained in the HGU dataset
data(SPIKE_INB)data(SPIKE_INB)
names of the Bacteria probe-sets contained in the HGU dataset
E. Carlon and T. Heim, Physica A 362, 433 (2006).
Ivsc, IvsDG, collapse, SPIKE_IN, hgu
, SPIKE_INA, SPIKE_INH
## you can first check if the data matches the predicted hybridisation value according to the langmuir ## value, from the intensity versus the concentration value Ivsc(SPIKE_INB[3]) ## you can then plot the value of the Intensity of the probe with the predicted value of the hybridisation ## according to the Delta G, value IvsDG(SPIKE_INB[4],64) ## The collapse function will finally plot all the values of the probe set according to ## the langmuir absorption theory collapse(SPIKE_INB[2]) ## By comparing the matched value and the mismatches, you will be able to identify errors which ## could have done while sampling the data, or if the error happens repeatedly this will show errors ## which will have happened while sequencing old data.## you can first check if the data matches the predicted hybridisation value according to the langmuir ## value, from the intensity versus the concentration value Ivsc(SPIKE_INB[3]) ## you can then plot the value of the Intensity of the probe with the predicted value of the hybridisation ## according to the Delta G, value IvsDG(SPIKE_INB[4],64) ## The collapse function will finally plot all the values of the probe set according to ## the langmuir absorption theory collapse(SPIKE_INB[2]) ## By comparing the matched value and the mismatches, you will be able to identify errors which ## could have done while sampling the data, or if the error happens repeatedly this will show errors ## which will have happened while sequencing old data.
This dataset contains the names of the Human probe-sets contained in the HGU dataset
data(SPIKE_INH)data(SPIKE_INH)
names of the human probe-sets contained in the HGU dataset
E. Carlon and T. Heim, Physica A 362, 433 (2006).
Ivsc, IvsDG, collapse, SPIKE_IN, hgu
, SPIKE_INA, SPIKE_INB
## you can first check if the data matches the predicted hybridisation value according to the langmuir ## value, from the intensity versus the concentration value Ivsc(SPIKE_INH[3]) ## you can then plot the value of the Intensity of the probe with the predicted value of the hybridisation ## according to the Delta G, value IvsDG(SPIKE_INH[5],256) ## The collapse function will finally plot all the values of the probe set according to ## the langmuir absorption theory collapse(SPIKE_INH[2]) ## By comparing the matched value and the mismatches, you will be able to identify errors which ## could have done while sampling the data, or if the error happens repeatedly this will show errors ## which will have happened while sequencing old data.## you can first check if the data matches the predicted hybridisation value according to the langmuir ## value, from the intensity versus the concentration value Ivsc(SPIKE_INH[3]) ## you can then plot the value of the Intensity of the probe with the predicted value of the hybridisation ## according to the Delta G, value IvsDG(SPIKE_INH[5],256) ## The collapse function will finally plot all the values of the probe set according to ## the langmuir absorption theory collapse(SPIKE_INH[2]) ## By comparing the matched value and the mismatches, you will be able to identify errors which ## could have done while sampling the data, or if the error happens repeatedly this will show errors ## which will have happened while sequencing old data.