read.eisen: Read expression data from a file formatted for Eisen...
In ctc: Cluster and Tree Conversion.
Description
Usage
Arguments
Details
Value
Author(s)
References
Description
The input for Eisen-clustering is a slight variation of a tab
delimited file. This method reads the expression data from such files as
a matrix and provides optional additional information on the experiments
as attributes.
Usage
1
read.eisen(file,sep="\t",dec=".", format.check = TRUE)
Arguments
file
The relative or absolute path to the file to be read, as
internally forwarded to the read.table function.
sep
Separator of fields, passed on to read.table.
dec
Passed on to read.table. This is particulary helpful for
the interpretation of data from localised spreadsheet programs.
format.check
TRUE or FLASE: to disable file format check.
Details
The software of Michael Eisen and its plain tab separated format for
the presentation of gene expression data prior to their clustering is
supported by many hard- and software providers, both as an input for
their tools and as resulting from the analysis and normalisation of the
chip images. To be able to read and write this format, the Bioconductor
suite is enabled to easily reanalyse or extend older experiments that
might have been analysed with the Eisen tools before.
Value
A numerical matrix is returned. It is a complete analogue of the
Eisen-format,
except the descriptions, weights and other information being passed to
attributes.
The first row will be the column names, the first column will be the
respective row name.
A second row that has a first empty field is referred to via the
attribute "second.row".
A column NAME is stored in the attribute "NAME".
Author(s)
Steffen Moeller
References
Michael Eisen Lab http://rana.lbl.gov/
Michael Hoon's Cluster 3.0
http://bonsai.ims.u-tokyo.ac.jp/~mdehoon/software/cluster/
Eisen M.B., P.T. Spellman, P.O. Brown, and D. Botstein. 1998.
Cluster analysis and display of genome-wide expression patterns.
/Proc. Natl. Acad. Sci. USA /, 95:14863-14868.
De Hoon M.J.L., S. Imoto, J. Nolan, and S. Miyano. Open source
clustering software. Bioinformatics *20* (9): 1453–1454 (2004).
Antoine Lucas and Sylvain Jasson, Using amap and ctc Packages
for Huge Clustering, R News, 2006, vol 6, issue 5 pages 58-60.
ctc documentation built on Nov. 8, 2020, 5:11 p.m.
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Description Usage Arguments Details Value Author(s) References
Description
The input for Eisen-clustering is a slight variation of a tab delimited file. This method reads the expression data from such files as a matrix and provides optional additional information on the experiments as attributes.
Usage
1 | read.eisen(file,sep="\t",dec=".", format.check = TRUE)
|
Arguments
file |
The relative or absolute path to the file to be read, as internally forwarded to the read.table function. |
sep |
Separator of fields, passed on to read.table. |
dec |
Passed on to read.table. This is particulary helpful for the interpretation of data from localised spreadsheet programs. |
format.check |
TRUE or FLASE: to disable file format check. |
Details
The software of Michael Eisen and its plain tab separated format for the presentation of gene expression data prior to their clustering is supported by many hard- and software providers, both as an input for their tools and as resulting from the analysis and normalisation of the chip images. To be able to read and write this format, the Bioconductor suite is enabled to easily reanalyse or extend older experiments that might have been analysed with the Eisen tools before.
Value
A numerical matrix is returned. It is a complete analogue of the Eisen-format, except the descriptions, weights and other information being passed to attributes. The first row will be the column names, the first column will be the respective row name. A second row that has a first empty field is referred to via the attribute "second.row". A column NAME is stored in the attribute "NAME".
Author(s)
Steffen Moeller
References
Michael Eisen Lab http://rana.lbl.gov/
Michael Hoon's Cluster 3.0 http://bonsai.ims.u-tokyo.ac.jp/~mdehoon/software/cluster/
Eisen M.B., P.T. Spellman, P.O. Brown, and D. Botstein. 1998. Cluster analysis and display of genome-wide expression patterns. /Proc. Natl. Acad. Sci. USA /, 95:14863-14868.
De Hoon M.J.L., S. Imoto, J. Nolan, and S. Miyano. Open source clustering software. Bioinformatics *20* (9): 1453–1454 (2004).
Antoine Lucas and Sylvain Jasson, Using amap and ctc Packages for Huge Clustering, R News, 2006, vol 6, issue 5 pages 58-60.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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