The advanced file importer enables the import of files from different sources to create input files that are suitable for cellHTS2 analysis.
Starting the advanced file importer
The advanced file importer can be accessed through clicking on the corresponding link in step 2 (plate file upload).
The link will open a new page:
Uploading text data files
Clicking on "Upload" button opens form that allows the selection of multiple files by using Ctrl + arrowkeys or Shift + mouse selection (requires FLASH player to work properly). Files could be either plate reader files or a complete table with all raw data and annotation information.
If you cannot multiselect files on this page, please install the Adobe FLASH Plug-in and restart your browser. Please note: the multi-upload feature will recognize empty or in case files are to large.
Imported data file need to be complete (no missing wells) and should only contain numerical data in the data columns. Data should be sorted by plate and well position.
The maximum upload file size is limited to 3MB
Some users reported that the upload field is not displayed. This appears to be caused by a bug in the 64bit FLASH plugin (which is still experimental). If you see the following screen without an upload button you probably do not have a stable 64-bit linux FLASH version. Clearing the cache/temporary files and restarting the browser is temporary solution. This is only a temporary fix until a stable version of the FLASH plug-in is available.
If you want to delete uploaded files and reset all settings you have made in the advanced file importer page, click on the "Delete all uploaded Files" button. Please note: because the advanced file importer can upload multiple file, the use of ZIP archives has been disabled. In order to upload ZIP archives, use the normal data file uploader (Step 2 in the web cellHTS workflow)
Reformatting text data files
As a next step, the importer needs additional information how different columns in the data files need to be interpreted. The importer can deal with both header and headerless files. Please note: All of your uploaded datafiles should be in the same header and file format.
A headerline is defined as the first line in the file which contains information about the column names. Shown below are examples of data files without and with a header line:
Next, it needs to be defined whether the files contain single or dual channel, and how replicates have been performed.
For text imports, it has further to be defined, which delimiter seperates different columns in the uploaded files. Typical delimeters are "\t" for tab, "\s" for whitespaces, ";" for semicolon separated and "," for csv-Files.
Next, click the Format data to process the files. A table will show the assigned columns for the first uploaded file. The program attempts to automatically assign header lines which can be later changed by the user.
Uploading Excel data files
The file uploader also handles Excel files to be automatically processed into cellHTS2 compatible file formats (Excel 95-2003 are permissible file formats).
Creating data files
To create cellhts2 compatible data files, at least three columns containing plate, well and raw value information needs to be mapped.
All three columns are essential for creating plate data files.
The importer tool will also check if well and value column are valid. For example a valid well column will be "A01", "A02", etc. A valid value column should be a non-letter integer or floating point number e.g. -10102.22
If there were problems with importing the data files, an error message will be shown.
Creating plate configuration and annotation files
The Advanced File Importer can also create suitable plate configuration and annotation data files, if such data has been provided in one of the files during import (e.g. a previous topTable or an Excel file that contained additional information).
Two Select boxes will be shown to create the cellHTS2 compatible files:
1. A cellHTS2 compatible plate config file required information plate, well and well annotation information (e.g. whether wells contain sample, positive or negative control reagents). Since we already have selected the appropriate plate and well, the user can now select the appropriate column that contains the well annotation. After clicking Create files, a suitable plat configuration file will be generated.
The well annotation column can only contain the following values: pos, neg, sample, other, empty, cont1, flagged, contaminated, cont
2. To create annotation files, map the appropriate column to the GeneID column. Further columns that should appear in the annotation (e.g. reagent IDs) can be added with the "Add further columns" tab. More then one column can be added by selecting new items. If all the selected entries should be removed, select Drop all.
Transfer generated files to the input queue of web cellHTS2
Next, click on import generated files to web cellHTS2 to confirm the newly generated files and add them to the input queue of web cellHTS2.
After you clicked on the import to cellHTS2 link all of your settings on the advanced file importer will be resetted
If only data files were imported, the user will be redirected to Step 2 in the analysis workflow to create the appropriate configuration files, otherwise it proceed to the last necessary step in the workflow.