aborg0 / hits Goto Github PK

What steps will reproduce the problem?
1. Create a heatmap view
2. Deselect some parameters or replicates
3. Change plate format or presentation

What is the expected output? What do you see instead?
Expected: the same options on the parameters/replicates,
but got: the actual parameter/replicate list

Quality report's metrics are wrong on the plate page if more than one
channel/parameter is measured. (Only the first column is correct.)

What steps will reproduce the problem?
1. Try to analyze an experiment with more than one parameters.

What is the expected output? What do you see instead?
Floating point outputs same as on the main screen.

It would be useful if there were colour codes for the legend parts.

It would be useful if the export functionality would save some context
(like colour coding as text) to the exported images.

What steps will reproduce the problem?
1. When launching the sample1 example after mapping all files from the 
svn/plate8 location, when launching the node cellHTS2, the Rserver starts 
working (loading libraries etc), but terminates, without completing.
2.
3.

What is the expected output? What do you see instead?
Not sure yet. It also appears that the screen log provided in the SVN is 
empty, although I am not sure whether it  optional, and what it is exactly 
for.

What version of the product are you using? On what operating system?
R2.9.0, followed installation procedure described in the wiki.
Surprisingly, I get a different output than expected with for the R 
library "cellHTS2":

> library("cellHTS2")
Loading required package: RColorBrewer
Loading required package: Biobase

Welcome to Bioconductor

  Vignettes contain introductory material. To view, type
  'openVignette()'. To cite Bioconductor, see
  'citation("Biobase")' and for packages 'citation(pkgname)'.

Loading required package: genefilter
Loading required package: splots
Loading required package: grid
Loading required package: vsn
Loading required package: hwriter
Scalable Robust Estimators with High Breakdown Point (version 0.5-01)


Please provide any additional information below.

Wen installing cellHTS2 in R I get the folwing message which seems to have 
some errors (inparticular with some incompatibilities between bioconductor 
and R2.9.0):
> source("http://bioconductor.org/biocLite.R")
> biocLite("cellHTS2")
Running biocinstall version 2.4.10 with R version 2.9.0 
Your version of R requires version 2.4 of Bioconductor.
Warning: unable to access index for repository 
http://brainarray.mbni.med.umich.edu/bioc/bin/windows/contrib/2.9
trying 
URL 'http://bioconductor.org/packages/2.4/bioc/bin/windows/contrib/2.9/cell
HTS2_2.8.0.zip'
Content type 'application/zip' length 3702776 bytes (3.5 Mb)
opened URL
downloaded 3.5 Mb

package 'cellHTS2' successfully unpacked and MD5 sums checked

The downloaded packages are in
        C:\Users\ghislain\AppData\Local\Temp\Rtmp4bKnjq\downloaded_packages
updating HTML package descriptions

What steps will reproduce the problem?
1. when clicking on a node (ex. simple onfigurator fo cellsHST2), in the 
node description, the link Details here. 
(about:../../help/simplePlateConfig.xhtml) does not link to an actua page
2.
3.

What is the expected output? What do you see instead?
A page withmore information.

What version of the product are you using? On what operating system?


Please provide any additional information below.

There should be a node to rank the score based on their values. Both for
increase and for decrease.

It would be useful if the user could see what does that normalisation,
scoring and summarisation methods are doing.

For some experiments the plates are not filled at every place. It would be
convenient if the read and analysis would not require to have full plates.

The recursive visit to folders would be useful in some cases.

What steps will reproduce the problem?
1. Installing the feature
2.
3.

What is the expected output? What do you see instead?
The node does not install.

What version of the product are you using? On what operating system?
Lattest version of HITS/KNIME on eclipse 3.5

Please provide any additional information below.


When trying to install this feature I receive the following error:

Cannot complete the install because of a conflicting dependency.
  Software being installed: HiTS imaging feature 0.0.1.200909291756 
(ie.tcd.imm.hits.image.feature.feature.group 0.0.1.200909291756)
  Software currently installed: HiTS interoperability with other projects 
0.0.1.200908202037 (ie.tcd.imm.hits.knime.interop.feature.feature.group 
0.0.1.200908202037)
  Only one of the following can be installed at once: 
    Common Plug-in for KNIME development 0.0.1.200908202037 
(ie.tcd.imm.hits.common 0.0.1.200908202037)
    ie.tcd.imm.hits.common 0.0.2.200909291756
  Cannot satisfy dependency:
    From: HiTS imaging feature 0.0.1.200909291756 
(ie.tcd.imm.hits.image.feature.feature.group 0.0.1.200909291756)
    To: ie.tcd.imm.hits.common [0.0.2.200909291756]
  Cannot satisfy dependency:
    From: HiTS interoperability with other projects 0.0.1.200908202037 
(ie.tcd.imm.hits.knime.interop.feature.feature.group 0.0.1.200908202037)
    To: ie.tcd.imm.hits.common [0.0.1.200908202037]

What steps will reproduce the problem?
1. Use column names with A, b, C (in this order)
2. Execute the CellHTS2 node with all of these parameters

What is the expected output? What do you see instead?
Expected:
the columns are in the A, b, C order, with the expected data in each column.
Got:
The columns are in the A, b, C order, though the contents are in (case
sensitive) alphabetically ordered.

Currently, installing of hits completely messes up my plugins-folder. Most
eclipse-plugins follow the same scheme. 

The problem is that currently only single, or replicate count
parameters/channels can be used.

What steps will reproduce the problem?
1. Start a 3 replicate experiment analysis with 2 or 4 parameters selected.

What is the expected output? What do you see instead?
The analyzed results are on the same result pages for all parameters. Have
scored heatmaps and toptable.

What steps will reproduce the problem?
1. Using Eclipse 3.4.2 and add the site to the update manager
2. Look for updates
3.

What is the expected output? What do you see instead?

You should see HITS in the update site available features. Only KNIME 
Utilitioes shows up. Using Eclipse 3.3.2 does not cause this problem. I 
suspect a problem with the way the update site.
Dropping: ie.tcd.imm.hits.feature_0.1.1.jar ; ie.tcd.imm.hits_0.1.1.jar ; 
ie.tcd.imm.hits.3rdparty_0.1.0.jar in eclipse dropins folder allows to get 
access to the KNIME nodes.

What version of the product are you using? On what operating system?
Eclipse 3.4.2 / Could not download HITS.

Please provide any additional information below.
Cf. attached image of the update manager.

It would be nice to have a node which creates the same results as cellHTS2
-at least for the less complex ones- to be easier to interpret the results,
and to be able to modify if necessary.

What steps will reproduce the problem?
1. Setup a simple cellHTS2 workflow
2. Try to add variance adjustment

What is the expected output? What do you see instead?
Expected: proper execution with the results.
I see: Problem with normalisation step.

No nodes without selected (true) knime expert mode flag depend on that
feature, so that should be optional.

What steps will reproduce the problem?
1. Run the CellHTS2 node

What is the expected output? What do you see instead?
It is expected to have the data from the description inport, but we get
only empty results.

It would be useful if the barcodes could be used on Plate Heatmap.

Please describe the purpose and the intended behaviour of the new feature.
Having some examples of pipeline (and data templates) using Hits would b 
extremely useful!
If it has connection to other parts please state it too.

Please describe the purpose and the intended behaviour of the new feature.
Some of the nodes are a bit hard to comprehand in particular without some 
specific examples. Perhaps, adding a link to some on-line examples would 
be a nice feature to have.

For instance in the upivot node, I was not sure how to get it to work. I 
figured out that you needed to add a capturing group and that the 
remainder would be the column name, but it would have been easier to 
figure out with some examples.

If it has connection to other parts please state it too.

Please describe the purpose and the intended behaviour of the new feature.
Most biological reaction follow a Sigmoidal/LogSigmoidal regression. 
Creating tool to calculate such regression such as EC50, Min, Max etc. 
would be great.

If it has connection to other parts please state it too.
I wanted to devellop such library but I don't know enough about KNIME to 
do it (in addition, I was having problem to get some of the HITS source 
code to use as a base).

For this I wanted to use Michael Thomas Flanagan's Java Scientific Library 
(http://www.ee.ucl.ac.uk/~mflanaga/java/ need to get permission to 
redistribute) which provides the tools to calculate Ec50 etc. An other 
resource that could work is: www.ncgc.nih.gov/pub/openhts/curvefit.

Note that it would be nice to be able to get this EC50 on sets with 
replicates and for multiple features measured.

For instance if you have a table as follow:

CompoundID;[Concentration];Value1;ValueX;etc
A;1;3;5;...
A;1;2;4;...
A;10;15;30;...
A;10;18;27;...
B;...

to obtain an EC50 (or other parameters of the sigmoid) for each of the 
compounds.

I think part of this can be done using KNIME nodes provided with Hits, but 
the Sigmoid or other type of regression and there plotting does not exist. 
Perhaps this could be done?

In CellHTS2 node it would be useful if there were an option to ask to
overwrite the results before actually overwrite them.

It is really annoying that the report generation might stop with a useless
error message during CellHTS2 node generation when one of the files to
generate has too long path.

It would be more user-friendly if there were a check in the configuration
part to prevent this behaviour.

Exception in thread "AWT-EventQueue-0" java.lang.ArrayIndexOutOfBoundsException: -1
at org.knime.core.data.container.BlobSupportDataRow.getCell(BlobSupportDataRow.java:144)
at com.mind_era.knime.util.view.dendrogram.viewonly.HeatmapDendrogramDrawingPane.paintContent(HeatmapDendrogramDrawingPane.java:192)
at org.knime.base.node.viz.plotter.AbstractDrawingPane.paintComponent(AbstractDrawingPane.java:159)
at javax.swing.JComponent.paint(JComponent.java:1053)
at javax.swing.JComponent.paintChildren(JComponent.java:886)
at javax.swing.JComponent.paint(JComponent.java:1062)
at javax.swing.JViewport.paint(JViewport.java:744)
at javax.swing.JComponent.paintChildren(JComponent.java:886)
at javax.swing.JComponent.paint(JComponent.java:1062)
at javax.swing.JComponent.paintChildren(JComponent.java:886)
at javax.swing.JComponent.paint(JComponent.java:1062)
at javax.swing.JComponent.paintChildren(JComponent.java:886)
at javax.swing.JComponent.paint(JComponent.java:1062)
at javax.swing.JComponent.paintChildren(JComponent.java:886)
at javax.swing.JComponent.paint(JComponent.java:1062)
at javax.swing.JLayeredPane.paint(JLayeredPane.java:586)
at javax.swing.JComponent.paintChildren(JComponent.java:886)
at javax.swing.JComponent.paint(JComponent.java:1062)
at javax.swing.JComponent.paintToOffscreen(JComponent.java:5217)
at javax.swing.RepaintManager$PaintManager.paintDoubleBuffered(RepaintManager.java:1532)
at javax.swing.RepaintManager$PaintManager.paint(RepaintManager.java:1455)
at javax.swing.RepaintManager.paint(RepaintManager.java:1252)
at javax.swing.JComponent._paintImmediately(JComponent.java:5165)
at javax.swing.JComponent.paintImmediately(JComponent.java:4976)
at javax.swing.RepaintManager$3.run(RepaintManager.java:811)
at javax.swing.RepaintManager$3.run(RepaintManager.java:794)
at java.security.AccessController.doPrivileged(Native Method)
at java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDomain.java:75)
at javax.swing.RepaintManager.paintDirtyRegions(RepaintManager.java:794)
at javax.swing.RepaintManager.paintDirtyRegions(RepaintManager.java:769)
at javax.swing.RepaintManager.prePaintDirtyRegions(RepaintManager.java:718)
at javax.swing.RepaintManager.access$1100(RepaintManager.java:62)
at javax.swing.RepaintManager$ProcessingRunnable.run(RepaintManager.java:1680)
at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:311)
at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:744)
at java.awt.EventQueue.access$400(EventQueue.java:97)
at java.awt.EventQueue$3.run(EventQueue.java:697)
at java.awt.EventQueue$3.run(EventQueue.java:691)
at java.security.AccessController.doPrivileged(Native Method)
at java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDomain.java:75)
at java.awt.EventQueue.dispatchEvent(EventQueue.java:714)
at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201)
at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116)
at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105)
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101)
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93)
at java.awt.EventDispatchThread.run(EventDispatchThread.java:82)

What steps will reproduce the problem?
1.Load table
2.Pivot
3.

What is the expected output? What do you see instead?
A table with the pivoted rows.

What version of the product are you using? On what operating system?


Please provide any additional information below.
I try to pivot the attached table.
Paramters for Pivot used: Pivot COlumn=ObjectIndex
Pattern: ${ObjectIndex}-${}
Behavior: fillEmpty


I receive the following warning and cannot evaluate the node:
WARN     Pivot   Not a nominal column: ObjectIndex

WHat am I doing wrong?

It would be useful to have a node which is able to generate the
configuration and the input data for the cellHTS2 program. This would
enable the check/publication of the results without the HiTS KNIME nodes.

Comparing different experiments would help to check the validity of a hit,
the comparison of normalization methods would make it easier to select the
proper one, see the differences between them.

What steps will reproduce the problem?
1.Installed KNIME 2.4.2, Rserve, locfit and newest cellHTS2 in R 2.13
2.Installed HiTS in KNIME and attempt to process plate reader data.
3.Following error:
ERROR    CellHTS2    Execute failed: This R installation has no supported cellHTS2 
installed.


What is the expected output? What do you see instead?


What version of the product are you using? On what operating system?


Please provide any additional information below.

What steps will reproduce the problem?
1. when clicking on a node (ex. simple onfigurator fo cellsHST2), in the 
node description, the link Details here. 
(about:../../help/simplePlateConfig.xhtml) does not link to an actua page
2.
3.

What is the expected output? What do you see instead?
A page withmore information.

What version of the product are you using? On what operating system?


Please provide any additional information below.

The CellHTS2 node now gives a clue where were the problem, but the actual
problem remains hidden.

It would be nice if all voidEvals would be replaced with a code like this:
RExpr e = conn.eval("try(" + command + ")");
//Check whether it is an error or not, if error report it with a meaningful
error message extracted from the expression.

It would be useful if there were a place where the heatmap colouring could
be changed. (For each statistic type, and each parameters.)