Difference between revisions of "Known Issues"
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** There is an easy work-around. After downloading data from caArray, and optionally setting up any needed groups of arrays or markers (e.g. treatment groups, controls etc), save the dataset as file type "Exp" format. You can then reload that saved dataset and associate the annotation file at that time. | ** There is an easy work-around. After downloading data from caArray, and optionally setting up any needed groups of arrays or markers (e.g. treatment groups, controls etc), save the dataset as file type "Exp" format. You can then reload that saved dataset and associate the annotation file at that time. | ||
* caArray - Data downloaded from caArray is being stored in a way that uses a large amount of memory, limiting the size of the dataset that can be used. Bug 1930. | * caArray - Data downloaded from caArray is being stored in a way that uses a large amount of memory, limiting the size of the dataset that can be used. Bug 1930. | ||
| + | ** The first work-around is to increase the amount of memory allocated to geWorkbench. | ||
| + | ** A second work around, if the first is impractical, is to download the data in reasonable sized sets of arrays and then save each set as an "Exp" format file. Delete the downloaded data set in geWorkbench and download the next set from caArray until all data has been saved to "Exp" files. | ||
| + | ** The Exp files can then be all read back in together and merged (make sure to check the "merge" check-box). | ||
* caArray - Data downloads from instances of caArray housed at the NCI can be very slow. This is apparently due to networking issues at NCI. Data downloads from local instances of caArray to geWorkbench are very fast. | * caArray - Data downloads from instances of caArray housed at the NCI can be very slow. This is apparently due to networking issues at NCI. Data downloads from local instances of caArray to geWorkbench are very fast. | ||
Revision as of 13:36, 24 July 2009
General
- Filtering a dataset to remove values marked as "missing" may invalidate objects that arose from the original, unfiltered dataset. Any filtering should be done before any analysis which creates child result nodes, e.g. a t-test, ANOVA etc.
geWorkbench 1.7.0
- Annotations - The retrieval of annotations using the Marker Annotations component does not work for microarray data downloaded from caArray. Bug 1956.
- There is an easy work-around. After downloading data from caArray, and optionally setting up any needed groups of arrays or markers (e.g. treatment groups, controls etc), save the dataset as file type "Exp" format. You can then reload that saved dataset and associate the annotation file at that time.
- caArray - Data downloaded from caArray is being stored in a way that uses a large amount of memory, limiting the size of the dataset that can be used. Bug 1930.
- The first work-around is to increase the amount of memory allocated to geWorkbench.
- A second work around, if the first is impractical, is to download the data in reasonable sized sets of arrays and then save each set as an "Exp" format file. Delete the downloaded data set in geWorkbench and download the next set from caArray until all data has been saved to "Exp" files.
- The Exp files can then be all read back in together and merged (make sure to check the "merge" check-box).
- caArray - Data downloads from instances of caArray housed at the NCI can be very slow. This is apparently due to networking issues at NCI. Data downloads from local instances of caArray to geWorkbench are very fast.
