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Generate MapMan Experimental Data Set Inquiry

Generate MapMan Experimental Data Set Inquiry
mapman input format file experimental data set
Answer
6/20/16 10:28 AM
I have 5 biological replicates of healthy and infected Cacao seedlings plant.
I done the mapping of 5 biological replicates of healthy and 5 biological replicates of infected Cacao RNA-seq against gene model of cacao (downloaded from Cacao Genome Database) by using RSEM.
I have the expression file for each RNA-seq data set now.

I have run the Mercator (by using gene model of cacao as input) to generate Mappings file for MapMan.
For Pathway, I will choose existing "Metabolism_overview" in MapMan.

Can I know how to use my expression file from 5 biological replicates of healthy and 5 biological replicates of infected Cacao RNA-seq against gene model of cacao to generate MapMan Experimental Data Set?

I would like to upload my own Mapping file (output of Mercator) and my own Experimental Data Set in MapMan.
I have read the MapMan manual, I still not too sure how to generate own Experimental Data Set by using expression result as an input.
Thanks a lot and looking forward to hear from your advice.

RE: Generate MapMan Experimental Data Set Inquiry
Answer
6/23/16 3:57 AM as a reply to CHIA JING YI.
Any advice regarding my inquiry?
Thanks.

RE: Generate MapMan Experimental Data Set Inquiry
Answer
8/30/16 9:17 AM as a reply to CHIA JING YI.
HI

sorry for the late reply. You would use DESeq2 or edgeR or similar to generate log2 fold changes and flags for differential expression. Then you would create a file like this


(three columns)
ID log2FChealthy_vs_treated d_og2FChealthy_vs_treated
a112 -1.2 1

You can name the last column as you like but if you add d_ at the front it autoconfigures. In this columns you can addd
1 significantly up -1 singicinatly down 0 not changed.

Best
Björn

RE: Generate MapMan Experimental Data Set Inquiry
signicant
Answer
9/1/16 3:59 PM as a reply to Björn Usadel.
Dear Professor Björn,

Thanks a lot for your advice.

May I know that is the three column should be:
(three columns)
ID log2FChealthy_vs_treated d_log2FChealthy_vs_treated
a112 -1.2 1

Instead of

(three columns)
ID log2FChealthy_vs_treated d_og2FChealthy_vs_treated
a112 -1.2 1

Is there a grammar mistake at above?
Apart from that, regarding "1 significantly up -1 singicinatly down 0 not changed" that you mentioned.
May I know the
Significant up, 1 is refer to gene expression of healthy > gene expression of treated or gene expression of treated > gene expression of healthy;
Significant down, -1 is refer to gene expression of healthy > gene expression of treated or gene expression of treated > gene expression of healthy;
0, not changed, is it refer to gene expression that no significant different?

May I know what is the default cut-off in MapMan to determine as Significant up/down?
I have read some journal is refer to Padj < 0.05 or Padj < 1e-10 etc.

Thanks a lot and again for your advice.

RE: Generate MapMan Experimental Data Set Inquiry
Answer
9/6/16 9:37 AM as a reply to CHIA JING YI.
Hi

yes indeed that was a typo.
MapMan just uses data that you prefilter, thus the choice of FDR p-value and what you consider significant is up to you. Usually with FDR control, people would use 0.05 (5%) still, sometimes even 0.1.

For + and - it depends as it does for your log2 fold change.
If you say I compare infected versus healthy this translates (very simplified) into log2 value Infected MINUS log2 value healthy
and the significance indicaor would change accordingly

However it is equally ok to say that you compare healthy versus infected so the sign changes....

Björn

RE: Generate MapMan Experimental Data Set Inquiry
Answer
9/6/16 3:10 PM as a reply to Björn Usadel.
Dear Professor,

Thanks a lot and again for your advice.

Let me have a try to run on it.
I will get back to you soon.

Thanks a lot and again.