I have been using MapMan using the experiments, maps, and pathways provided in the download.  I am now hoping to use it on a dataset that I obtained from apple and have compared with cold-regulated genes in Arabidopsis (lists that are available through the Hannah, et al paper in PLoS Genetics).  

I am confused about the use of maps and bincodes.  I have downloaded several of the maps from the MapMan website but am confused when or how to use them.  It seems that the only map that will work is the Affy map, otherwise the program indicates that it does not have bincodes associated with the maps (or the data?).  Yet in the help manual it states that different images need different mapping files.

Could someone clarify briefly how and when to use the alternative maps (other than the Affy Map) and how does one assign bin codes (something is mentioned about Scavenger module. Is this something that is accessible as a download?)

Your assistance is greatly appreciated.

Hi,

the pictures of pathways or overviews are generic, they just indicate which "bins" have to be shown there.
A bin is something relating functional processes.
The so-called mapping file (mappings node) "maps" genes into bins and is currently available for Arabidopis, tomato, potato, chlamydomonas and others.

If you want to use: Arabidopis genecodes you need to use an Arabidopis gencode mapping file e.g. ath_tair_version

If you want to use affy code you use ath_affy_version

And apple (if we had it) probably msy_XXX_version


Best Wishes,
Björn

Bjorn,

Thanks again for your prompt reply. I appreciate your response and your answer reflected my understanding. I have the Affy Tair 7 and the AGI Tair 7 mappings in my directly. When I use one of the sample experimental sets (eg. Nitrogen starvation) it will only show gene expression data on the metabolic pathway figures if I have selected the AFFY TAir 7 mapping. If I choose the AGI Tair 7 and select the nitrogen starvation (or other sample experimental data), the metabolic figures come up but no gene expression data. the same is true if I pick a different metabolic figure such as regulation overview. That is where my confusion lies. It seems that since I am working with Ath data in both cases that either mapping selection should work.

I appreciate your patience with these rather basic questions. Perhaps a step by step tutorial on the website would help.

thanks again,

Michael

I understand your confusion regarding the use of maps and bincodes in MapMan. It can be a bit overwhelming when you have different maps available and are unsure about when and how to use them effectively.

Regarding the maps in MapMan, the Affy map is commonly used and has associated bincodes, which is why it works seamlessly with the program. However, it's important to note that other maps can be used as well, depending on the specific dataset and analysis requirements.

To use alternative maps in MapMan, you need to ensure that the chosen map has compatible bincodes associated with it. Some maps may not have bincodes readily available, which could be why the program indicates a lack of association between the maps and data. In such cases, you might need to assign bin codes manually or through additional tools like the Scavenger module.

The Scavenger module can be a helpful resource for assigning bin codes and making use of alternative maps. It allows you to create custom maps or modify existing ones to suit your specific needs. However, please note that the availability of the Scavenger module as a download may depend on the version and specific installation of MapMan you are using. You may need to check the MapMan website or consult the program's documentation for information on accessing the Scavenger module.

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If you require further assistance or have additional questions, please feel free to ask. We are here to help you navigate through any challenges you encounter while using MapMan.

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