ArrayPipe Help

  • Action Chain
    In the table below you can choose the type of actions and the order in which they are applied to your data. It starts with the top left and ends at the bottom right. Empty fields are skipped. Leave space (= empty fields) between your actions to be able to add more steps later.

  • Action Settings
    The actions that were applied in the last step are listed at the bottom of the page. You can modify them by adding or deleting steps, or changing their order.

  • Add Links
    If your data contains annotation columns, these can be enriched with links to external sources. Otherwise this selection box is empty.

  • Array Layout
    Normally, arrays are divided into subgrids that are specified as meta rows x meta columns, and each subgrid contains rows x columns spots. Please specify the layout below (MCOL = meta columns, etc.).

  • Authentication
    Right after the login you will be asked again by the web-server for your username and password.

  • Range
    You can choose to do a barplot of only the data that you see on this page (visible) or of all entries in the data file (all).

  • Channel Assignment (Label and Annotation)
    You can choose which label to give each channel (this is also another way of specifying a dye swap).
    Some modules might need to know if a channel carries the signal of a control or of a treatment. This can be assigned in this column with the letters 'C' and 'T'.
    To distinguish replicates from different controls or treatments, add numbers to the letters, e.g. T1 and T2 would be regarded as two different treatments, but T3 and T3 would refer to treatment 3 and its replicate.
    Note: This feature is still experimental!

  • Output Name
    By default the program stores each project under a directory consisting of a number (e.g. '_22981'. This text field allows you to make this name more meaningful (e.g. 'batch 1 normalization'). This will be activated the next time the 'Do It' button is clicked. (Blanks will be replaced by underscores.)

  • Chunk Size
    The output can be divided into chunks of a specified size to make handling of otherwise large tables easier.

  • Clear Button
    Click this button to clear the action menu.

  • Column Headers
    The program needs to know which column headers are used for spot labels (Spot ID), foreground intensities (FG), and background intensities (BG). The intensities should be reported individually for each channel (CH1, CH2).
    The Spot ID can be set to 'undefined' in which case only the spot positions are used, assigning them in the order they are read in, from top left corner to the bottom right of the slide.

  • Data Auto Detection
    For known file types, such as ArrayVision or ImaGene, the program knows which columns contain the important data, such as foreground intensities and flags. For other types of files it is only guessing and you might need to specify the right columns.
    For the array layout, the program tries to guess fitting parameters from the number of data rows. Please check that they are correct.

  • Data Input
    There are currently two ways to submit data to the pipeline:
    1. Upload files directly from your computer.
    2. Pick one or more of the provided examples (if available).

  • Data Input Modification
    If you decide to remove one of the files you have worked on (for example, if it is flawed or skews the results) or if you wish to add more files to your current selection you can do so. There is also the option to upload gene lists to overlay them onto the data.

  • Do It Button
    Click this button to start processing the data.

  • Example Files
    Your pipeline operator might have provided some example files for you, in which case they will be listed below. Tick the boxes of those files you would like to work on and click the 'Load Files!'-button.

  • File Compression
    To reduce the upload time, you can compress one or more files into a ZIP archive or compress and bundle them with gzip and tar on Linux.

  • Operators
    The operators '>', '>=', '<', and '<=' only work for numbers.
    The operator '=' can be used for both numbers and text, whereas in the latter case only an exact match will trigger a filter action.
    You can use the '//' operator for regular expressions, i.e. 'AC\d{1,4} (foo|bar)' would match the string 'AC' followed by one to four digits, then a space and then either a 'foo' or a 'bar'.

  • Flag Column
    Specify the column header(s) that contain flagging information (either assigned automatically by the image quantification software, or added manually). To ignore all flags, set to 'undefined'.

  • Header Repeat
    Normally, a header is printed at the beginning and end of each chunk. For more frequent headers, specify a number which forces printing of a header line after that many lines of output.

  • Hide Columns
    Mark the headers of the columns that you would like to hide in the output.

  • Input Files
    You can upload output files from ImaGene, ScanArray, GenePix or ArrayVision. Simple tab-delimited files with a one-line column header should work in most cases.

  • Input Lists
    You can upload files that specify a selection of spots via grid coordinates or label names. There are several possibilities to specify reporters:
    • write down the spot or oligo ids (one item per line)
    • indicate the position with the coordinates MROW,MCO,ROW, and COL (separated by TABs, one entry per line)
    • use lists generated by ArrayPipe

  • Line End
    Specify at which line in the data file to end the table display.

  • Line Start
    Specify at which line in the data file to start the table display.

  • Lines Column
    This column shows the lines found in the input file (data + header + comments).

  • 'Load Files and Do it' - Button
    For a quick way to repeat a process on additional files, specify the data to load and click this button.

  • ArrayPipe Login
    To protect your data from others, login with your username and password. Choose something that's easy to remember and not so easy to guess, but please don't use important passwords because they might be visible to the operators of the program. Any data uploaded and generated after login will only be accessible with the correct username and password (Note: these are case-sensitive!).

  • Gene List Match
    This column shows the the number of times that the items of each gene list match within each data file.

  • Parameter Settings
    The parameter section contains a listing for each action with explanatory information and mechanisms to change the parameters.

  • Popup Boxes
    Wherever you see this sign you can get a popup box with additional information when you hover with your mouse over it. It will dissappear again when you move your mouse away. This feature needs Javascript to be activated.
    You can also click on the link, which will open up a new window with the help text. This should work for all browsers.

  • Public Entry
    For this entry mode you don't need a username or password. Your data will be stored in public space.
    Simply click on 'Enter' to continue.

  • Refine Button
    Click this button to refine the parameters for each action step (Experimental!).

  • Automatic Page Loading
    The browser will reload the results page automatically in intervals that are approximately equivalent to the execution time of each processing step. This mechanism helps overcome time-out problems for long processes and enables viewing of partial results as soon as they become available.

  • Reset Button
    Click this button to reset the page to its original state.

  • Rounding
    To reduce the number of digits after the decimal point, select how many positions to round to. This applies to all cells in the table output that contain numbers only.

  • Save Settings Button
    Click this button to save your settings (parameters and action chain) under the name specified in the text box to the right (add a note if you like).

  • Listing
    Specify how many entries you would like to have listed (in addition to the barplot/histogram). Use '0' for no listing and 'all' for everything (this could get BIG).

  • Skip Flags
    !! to be generated within the program to get the proper definition of flags

  • Swap Channels
    Normally, the first column of intensities is assigned to channel 1 (CH1)and the next to channel 2 (CH2). Tick this box in case you would like to switch this around. This will affect the ratios, which are normally calculated CH2/CH1

  • Table Font
    Change this value to increase or decrease the font of the text in the output table.

  • Unload Files
    To unload one or more of your working files, tick this box. It will come into effect next time you press any of the '(Un)Load Files!' or '(Un)Load Files and Do it!' buttons.

  • 'Unoad Files and Do it' - Button
    For a quick way to repeat a process on fewer files, tick the 'unload' box for the files you would like to drop and click this button.

  • Upload Fields
    There is currently no limit for the number of files to be processed. If you wish to upload more files at one time than boxes available, please increase the field number and click the 'Change!'-button.

  • ArrayPipe Username
    An empty username or the username public does not require a password. Simply click the 'Enter' or 'Login' button. Data stored this way can be accessed by (and shared with) anyone within the project.

  • Web Files
    You can specify a URL to download files straight from the web. Ideally, these should be in ImaGene, ScanArray, GenePix or ArrayVision format, but simple tab-delimited files with a one-line column header should work in most cases.

last updated at Tue May 30 13:54:27 PDT 2006
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