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Old 11-18-2015, 12:25 AM   #19
frymor
Senior Member
 
Location: Germany

Join Date: May 2010
Posts: 149
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Yes, it helps a lot. I think I start understanding it.

I have another question about the colData. Does the order of the samples here must be the same as in the count table.
I am asking because I have done the analysis mentioned above and found no DE genes. When I than changed the colData file to that:

Code:
name	condition	stimulation
Vav_KO_1	KO	no
Vav_KO_2	KO	no
Vav_KO_5	KO	no
Vav_KO_2_C	KO	yes
Vav_KO_4_C	KO	yes
Vav_KO_5_C	KO	yes
Vav_WT_1	wildtype	no
Vav_WT_2	wildtype	no
Vav_WT_4	wildtype	no
Vav_WT_4_C	wildtype	yes
Vav_WT_1_C	wildtype	yes
Vav_WT_2_C	wildtype	yes
I suddenly get 106 genes with an adjp<=0.1

the sample names was not changed and is identical to the column names of the count table.
Now I also get a different last comparison possiblity:
Code:
> resultsNames(dds)
[1] "Intercept"                        "condition_wildtype_vs_KO"        
[3] "stimulation_yes_vs_no"            "conditionwildtype.stimulationyes"
compared to "conditionwildtype.stimulationnone" from before.
Is there an explanation for this kind of changes?

thanks in advance
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