Linux/Unix problems
CEL Files Loading Problems
How do I install R and the Bioconductor "affy" package?
Loading of CEL files or performing SAM filter continue for ever
Clustering
When I try to run Biclustering on my data I get a failure notice.
How can I save the clustering expression patterns charts?
Grouping Analysis (functional and promoter analysis)
When I run Functional Analysis, Expander gets stuck.
When I load a session with that contains Functional Analysis results, Expander gets stuck,
When I try to run the promoter\functional analysis, I get a failure message box.
Promoter\Functional analysis produces no results (the resulting view is empty).
How can I save the bar charts produced by Expander, displaying the enrichments?
Why do certain Transcription Factors have a few accession numbers or\and a few gene IDs?
Others
Answer: Make sure that you have write permission in the Expander directory, and execution permissions on the files: click.exe, samba.exe, annot_sets.exe and analyzeFingerprints.exe, which are under the Expander directory. If the problem still occurs, open the file expanderLog.txt and search for the text: “libstdc++.so.5”. If this text appears (along with a message indicating it has not been found), please contact your system administrator and report this problem (this is a system problem). If you do not have a system administrator, and fail to install this library, please contact us (expander@cs.tau.ac.il) and we will try to assist.
How do I install R and the Bioconductor "affy" package?
Answer: please refer to R External Application section.
Loading of CEL files or performing SAM filter continue forever.
Answer: If the operation continues forever (the 'processing, please wait' window is displayed), please check if there is a folder with a space in its name somewhere in the path of Expander (or the CEL files) directory. For example, if the name of the Expander folder is 'Expander 4', change it to 'Expander_4'. The R software used for preprocessing CEL files has a problem dealing with spaces in the path. If this is the problem, then in the expanderLog.txt file (in your Expander directory) there should be a message about arguments being ignored.
Loading of CEL files fail.
Answer: If you are working with Expander version 4, please update to 4.0.1 or higher. Make sure you have R along with the Bioconductor “affy” / "aroma.affymetrix" packages installed in the R version which is specified in the settings “External Applications” tab (from the menu select Options >> Settings >> External applications). If R location is not defined in the settings, please define it (In Windows, R.exe file is likely to be located in the 'bin' folder of R software. In Linux, you may type 'which R' in the command line to find R path). If loading of CEL files still fails, please make sure that the Files location which you specified in the 'Load CEL Files' dialog box, is a folder which contains CEL files and that you have write permission to that folder.
When I try to run Biclustering on my data I get a failure notice.
Answer: Make sure that the ‘Use option files of type’ field in the SAMBA input dialog box is not empty (if it is, please re-download Expander). Also make sure that the following files exist in your Expander directory: ibic.opt, samba.exe.
How can I save the clustering expression patterns charts?
When the clustering results tab is open, please go to File >> Save As Image.
When I run Functional Analysis, Expander gets stuck.
Answer: If you are working with Expander version 4.0 or 4.0.1, please update to a higher version (4.0.2 and on).
When I load a session with that contains Functional Analysis results, Expander gets stuck.
Answer: If you are working with Expander version 4.0 or 4.0.1 (and the session was created with a version < 4.0), please update to a higher version (4.0.2 and on).
Answer: Fingerprint files are not placed in the right directory. Fingerprint files should be placed under the ‘TF_fingerprints’ directory that is under the Expander/organism/<org name> directory. For example, the human FP file should be placed under: …/Expander/organisms/human/TF_fingerprints/. When downloading the organism specific data zip, it should be extracted into the Expander/organisms/ directory. This will automatically put them in the right place.
Group analysis (enrichment analysis) leads to a failure message box.
Answer: Errors while running group (enrichment) analysis can be caused by the following problems:
a) Organism specific data (Fingerprint\annotation files) is not in the right directory. The organism specific data zip should be extracted into the Expander/organisms/ directory. You may download the relevant data by selecting from the menu: Help >> Download Data for Organism.
b) Data contains elements that do not appear in the background set (this is only relevant when the background set is loaded from an external file).
Group analysis (enrichment analysis) produces no results (the resulting view is empty).
Answer: This can be caused by one of the following:
a) You are using the wrong conversion file or a conversion file that is not in the right format or does not map the probes to the expected type of gene Ids. The conversion file maps each probe ID in your data file to a gene ID that is used in the group analysis. A conversion file is required when the probe Ids in your data file do not match the ones in the enrichment files (for example annotation and TF_fingerprint files that we supply).
b) You did not set the organism field in the input dialog to the organism type of your data.
c) You are trying to analyze only one set (e.g. the filtered data set) which you are using also as background (in this case the analysis has no meaning since it is trying to detect enrichments in the cluster/bicluster in comparison to the background set).
d) You set the threshold p-value to be too strict (low).
e) Biological reason i.e., there is nothing to report regarding this specific clustering/biclustering solution or this gene sets data.
How can I save the bar charts produced by Expander, displaying the enrichments?
When the results tab is open, please go to File >> Save As Image.
Why do certain Transcription Factors have a few accession numbers or\and a few gene IDs?
Answer: The transcription factors (TFs) found enriched by Prima are presented in the following way:
Accession Num. in TRANSFAC DB [TF name]. For example, M00287[NF-Y]
It is possible that a TF will have a few accession numbers in TRANSFAC, which represent different PWMs (position weight matrices specify the probability for observing each nucleotide at each position of the binding site, based on a set of empirically validated binding sites of the respective TF).
It is also possible that a TF will have a few Entrez gene IDs, since a TF may be composed of a few proteins. For example, NF-Y is a trimer, composed of 3 subunits.
Expander is not designed for Mac OS. You can probably use it partially – without running its features that require the execution of exe files (CLICK, SAMBA, TANGO and PRIMA). The exe files are only suitable for Windows and Linux / Unix.
This section will be updated as we get user feedbacks and problems.
Please refer all questions/comments to Expander@cs.tau.ac.il.