The advanced file importer can be used to upload a variety of file formats to cellHTS2. The purpose of this module is to provide a user-friendly interface to generate the required input files for cellHTS2 from different sources.
We will demonstrate how to use the *Advanced File Importer to generate
- plate data files
- plate config files
- annotation file
from different tab-delimited text and Excel files.
Download and unpack demo data set
Demo data set
This tutorial required a demo data set which can be downloaded from here.
After unpacking you will find the following files:
Start web cellHTS2
Start web cellHTS2 here. At step 1: Select single channel, leave the channel names fluc, rluc, click next.
Start the Advanced file importer
At step 2: Click on the Advanced File Importer link.
this will open the advanced file importer page:
FLASH Player is required to be able to upload multiple files in one step. Otherwise, only a simple upload button will be shown
Import text files
As a next step, we import text data files. All to be imported files should have the same header format.
To start the upload, click on the *Upload" field. A dialog box will be opened that can be used to multi-select files (FLASH needs to be installed and enabled) but will allow you to upload multiple files.
Select the demo file directory and multi-select several files as indicated below. If FLASH is disabled, you only can select one file by one.
Select the following files
and click on the open button to upload:
You will see the progress and the status of the uploaded files, after a few seconds this info screen will disappear, only showing the number of uploaded files.
After these files have been selected, the format has to be set. Open the files with a text editor to confirm that they are text files, delimited by tab and without a header. The demo data set does not have replicate information (only one raw value channel).
We deselect the checkbox "Data Files contain Headlines such as Plate, Well, Replicate...", deselect "multi channel" checkbox, select "text" as the file format, leave the rest as it is and click on format data:
The following window will appear:
This seem pretty much what we wanted it to look like. Next, we have to tell web cellHTS2 which column the plate, well and value for our data file is. Because, no header information in the data files was included, we will select it like the following column:
If we now click on create files, all of the uploaded files will be processed, the plate column of every line will be looked for unique plate names and plate numbers will be calculated for those. Because we have 4 different plate ids in the first file and uploaded 3 other files it will generate 4+3 = 7 plate data files.
If we leave the other drop down menus empty and click on the link "import generated files to web cellHTS2" we will be redirected to step 2 and all the files will be recognized in the platelist editor of web cellHTS2 and can be used for our analysis:
Normal upload file should not be combined with the Advanced File Importer files! Even if we could upload further files through the normal plate file upload, this is generally not a good idea because the plate/channel/replicate numbers will most likely be mixed up . You should use either the normal or the advanced file importer for your full data file set.
Upload of Excel files
Click on drop all entries go back to Step 1 in the analysis workflow, select dual channel instead of single channel like in the first tutorial, then go to Step 2 and click again on the Advanced File Importer Link to upload an Excel file.
In this example we will upload an excel file called toptable.xls which is an excel 97-2004 workbook which is a valid and supported file format in web cellHTS2.
This file contains multi plates, multichannel, and multireplicate data.
So we will upload the file and use the following settings:
and then click on "format data"
The following window will appear showing that or settings were successful:
So now make all your settings like shown here and click on the create files in the first two boxes (do not press it in the annotation box yet) to generate plate data files and plate config file:
Now we want to generate a Annotation file.
A annotation file only needs the GeneID column to create but often it is useful to add further columns. To do so click
select columns as long as you like from the "add further column" drop down box.
To clear your selected entries use the "drop all" selection.
After you have selected some fields click on the create files to create the file and then on the "import generated files to web cellHTS2" to make your generated files accessible in web cellHTS2.
After you have clicked on the link you will be redirected to web cellHTS2 where you can go on with setting up an analysis run (plate data files, plate config file and annotation file have been generated and submitted to the interface).