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 ask for Functional Analysis, no values appear in the Annotation type field of the input dialog box.
When I try to run the promoter\functional analysis, I get a failure message box.
Promoter\Functional analysis produce 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: This problem is caused due to a bug in version 3 that was fixed in version 3.1.1. The corrected version can be found in the download page (can be accessed directly by clicking the Help button à Open download page, or by opening the file "updates.html" that is in your existing Expander directory).
If you already have version 3.1 or a more updated version, you can simply use the update zip file and extract it into the existing Expander directory. Otherwise, it is best to re-download the most updated version.
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 ask for Functional Analysis, no values appear in the Annotation type field of the input dialog box.
Answer: Annotation files are not placed in the right directory. Annotation files should be located under the "annots" directory, that is under the Expander/organism/<org name> directory. For example, the human annotation files should be placed under: …/Expander/organisms/human/annots/. 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.
When I try to run Promoter Analysis no values appear in the Fingerprints file field of the input dialog box.
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.
When I try to run the promoter\functional analysis, I get a failure message box.
Answer: Errors while running promoter\functional 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.
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).
Promoter\Functional analysis produce no results (the resulting view is empty).
Answer: This can be caused by one of the following:
a) You forgot to load a conversion file along with your data file. The conversion file maps each probe ID in your data file to a gene ID that is used in the promoter and functional analysis. It is requires if the probe Ids that you are using in your data file do not match the ones in the annotation and TF_fingerprint we supply.
b) You did not set the organism field in the input dialog to the organism type of your data.
c) You have only one cluster 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.
When I select the ”Open an additional data sheet…” option in the “Confirm operation” dialog box (which appears when attempting a preprocessing operation after visualizations exist), nothing happens.
Answer: This problem is caused due to a bug in version 3.1 that was fixed in version 3.1.1. The corrected version can be found in the download page (can be accessed directly by clicking the Help button à Open download page, or by opening the file "updates.html" that is in your existing Expander directory).
If you already have version 3.1 or later, then you can simply use the update zip file and extract it into the existing Expander directory. Otherwise, it is best to re-download the current version of Expander.
This section will be updated as we get user feedbacks and problems.
Please refer all questions/comments to expander@cs.tau.ac.il.