Looking for a Unix command / tool that would convert PCL files into PDF files. I’ve searched the forum and the web and can’t find any. Is it even possible?. Hello. Environment: IBM AIX 6,1, power server. I have used Ghostscript tool ( gs) to convert a A4 LANDSCAPE PDF File to a PCL File, gs -q. NRW to TIFF,; ORF to TIFF,; OTB to TIFF,; OTF to TIFF,; PAL to TIFF,; PALM to TIFF,; PAM to TIFF,; PBM to TIFF,; PCD to TIFF,; PCDS to TIFF,; PCL to TIFF,; PCT .
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For sample data sets, click here. When creating files for GSEA, do not use hypens – in the file names. The GCT format is a tab delimited file format that describes an expression dataset. It is organized as follows:. The first line contains the version string and is always the same for this file format. Therefore, the first line must be as follows: The second line contains numbers indicating the size of the data table that is contained in the remainder of the file.
Note that the name and description columns are not included in the number of data columns. The third line contains a list of identifiers for the samples associated with each of the columns in the remainder of the file.
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Name tab Description tab sample 1 name tab sample 2 name tab The remainder of the data file contains data for each of the genes. There is one row for each gene and one column for each of the samples. The number of rows and columns should agree with the number of rows and columns specified on line 2. Each row contains a name, a description, and an intensity value for each sample. Names and descriptions can contain spaces, but may not be empty. Intensity values may be missing. To specify a missing intensity value, leave the field empty: The RES file format is a tab delimited file format that describes an expression dataset.
Pc is organized as follows. The first line contains a list of labels identifying the samples associated with each of the columns in the remainder of the file. Description tab Accession tab sample 1 name tab tab sample 2 name tab tab The second line contains rachivos list of sample descriptions. Currently, GSEA ignores these descriptions. Our RES file creation tool places the sample data file name and scale factors in this row, as shown below.
The third line contains a number indicating the number of clnvertir in the data table that is contained in the remainder of the file. There is one row for each xrchivos and two columns for each of the samples. The first two fields in the row contain the description and name for each of the genes names and descriptions archivox contain spaces since fields are separated by tabs. The description field is optional but the tab following it is not.
Each sample has two pieces of data associated with it: The PCL file format is a tab delimited file format that describes an expression dataset. For more information, see Stanford pcl file format. The TXT format is a tab delimited file format that describes an expression dataset. The first line contains the labels Name and Description followed by the identifiers for each sample in the dataset. The Description column is intended to be optional, but there is currently a bug such that it is treated as required.
We hope to fix this in a future release. If you have no descriptions available, a value of NA will suffice. The remainder of the file contains data for each of the genes. There is one line for each gene. Each line contains the gene name, gene description, and a value for each sample in the dataset.
Gene names and descriptions can contain spaces since fields are separated by tabs. The CLS file format defines phenotype class or template labels and associates each sample in the expression data with a label. The CLS file format uses spaces or tabs to separate the fields. The CLS file format differs somewhat depending on whether you are defining categorical or continuous phenotypes.
Categorical labels define discrete phenotypes; for example, normal vs tumor. For categorical labels, the CLS file format is organized as follows:. The first line of a CLS file contains numbers indicating the number of samples and number of classes.
The second line in a CLS file contains a user-visible name for each class. These are the class names that appear in analysis reports. The line should begin with a pound sign followed by a space.
The third line contains convegtir class label for each sample. The class label can be the class name, a number, or a text string.
The first label used is assigned to the first class named on the second line; the second unique label is assigned to the second class named; and so on. The order of the convsrtir determines the association of class names and class arhcivos, even if the class labels are the same as the class names.
The number of class labels specified on this line should be the same as the number of samples specified in the first line. The number of unique class labels specified on this line should be the same as the number archvos classes specified in the first line. Continuous phenotypes are used for time series experiments or to find gene sets correlated with a gene of interest gene neighbors. A CLS file for continuous labels can contain one or more labels.
Data Formats and File Extensions Quick Reference
The following example shows a CLS file that defines two continuous labels: The remainder of the file defines the continuous phenotypes.
For a continuous phenotype label, the values for the samples define the phenotype profile. The relative change in the values defines the relative distance between points in the phenotype profile. In the example shown above, the sample values for the two phenotype labels are gene expression values.
The phenotype profile is the expression profile for a gene and is used to find gene sets correlated with that gene. For a time series experiment, you would choose sample values that define the desired expression profile. The example shown below assumes that you have five samples taken at 30 minute intervals.
The first phenotype label defines a phenotype profile that shows steadily increasing gene expression; the second defines a srchivos that shows an initial peak and then gradual decrease:. The GMX file format is a tab archigos file format that describes gene sets.
The GMX file format is organized as follows:. Each gene set is described by a name, a description, and the genes in the gene set. GSEA uses the description field to determine what hyperlink to provide in the report for the gene set description: The GMT file format is a tab delimited archibos format that describes gene sets.
The GMT file format is organized as follows:. The GRP files contain a single gene set in a simple newline-delimited text format. The GRP file format is organized as follows:. The MDB files contain an entire arcyivos set database.
The CHIP file contains annotation about a microarray. It should list the features i. While this file is not used directly in the GSEA algorithm, it is used to annotate the output results and may also be used to collapse each probe set in the expression dataset to a single gene vector. The first line contains column headings that identify the content of each column in the remainder of the file. The file must contain three column headings separated by tabs: If a gene set or chip annotation file contains a gene in the Alias column, GSEA automatically converts it to the gene in the Gene Symbol column.
The rest of the file contains data for each probe set ID used in the microarray. The RNK file contains a single, rank ordered gene list not gene set in a simple newline-delimited text format. It is used when you have a pre-ordered ranked list that you want to analyze with GSEA.
For instance, you might have used your favorite tTest-like statistic converitr produce a ranked ordered gene list from your dataset which you now want to test for enrichment.
Order of lines does not matter. It is important, however, that the second column will have numeric values – they will be used to rank order genes by GSEA. Retrieved from ” https: Views Page Discussion View source History. Personal tools Log in. Contents 1 Expression Data Formats 1.