separation of number of DE genes for one sample from output file obtain from ballgown.

Question

[fatimarasool135]

Hi,

I have use the ballgown for differential gene expression. I have the six sample in my data set. The final list of differential gene expression obtain from the ballgown contain no sample name information from which I can calculate the number of DE gene in corresponding samples. The list is as

feature id    fc     pval                qval
1   gene    MSTRG.54886 0.304864331 2.14E-11    7.36E-07

2   gene    MSTRG.20291 0.317939083 3.50E-07    0.005305344

3   gene    MSTRG.28511 0.188768117 5.69E-07    0.005305344

4   gene    MSTRG.54860 0.207911219 7.11E-07    0.005305344

5   gene    MSTRG.69745 0.24928575  7.71E-07    0.005305344

how I can get the information number of differential expressed genes in one sample and so in second , third and so on . Next question is that I want to plot the van diagram of this data set of DE genes. how I can do it.

Answer 1

[ATpoint]

You should really invest time to get a (better) idea what the tools you are using are actually doing and how statistical testing of counts works (at least in principle). In typical DE analysis you use replicates to get a group-level average of the expression per gene and an estimation of the biological variation within groups. The result is then the change of the average gene expression between groups but not for each single sample. To get information on each sample you would need a different experimental design having technical replicates for the same sample or do additional experiments such as RT-qPCR to test the RNA pool from that sample for some genes individually.

Answer 2

[WouterDeCoster]

how I can get the information number of differential expressed genes in one sample and so in second , third and so on .

You don't do differential expression per sample, but per groups of sample. So this is not a meaningful analysis. If there are specific genes you are interested in you could make a boxplot, violin plot or swarm plot to look at the expression per sample.

Next question is that I want to plot the van diagram of this data set of DE genes.

The venn diagram, you mean? What exactly do you want to plot?

[fatimarasool135]

Hi, I got it .I have made the two groups each contain the 3 samples in pheno_data file. Next I want to do Gene ontology and gene enrichment analysis. For gene ontology I try it on AgriGo. but this tool not take the genes id named as TraesCS3D02G273600. how can I do gene ontology of wheat.

I am new to this field and I have to do this project in all situation. kindly tell me on this last step of gene ontology. I have also read the manual to GOseq R based package for this step.