Defining the design matrix
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@humberto_munoz-10903
Last seen 7.7 years ago

 

I am defining my design matrix with the following results below.

> RG<-calcNormFactors(RG, method=c("TMM"),
+                 refColumn=1, logratioTrim=.3, sumTrim=0.05, doWeighting=TRUE,
+                 Acutoff=-1e10, p=0.75)
> RG$samples
              files group lib.size norm.factors
ARef1     ARef1.csv     1  2911652    1.1218729
ARef24   ARef24.csv     1  2911652    1.1218729
CO21       CO21.csv     2 11198918    1.0289838
CO224     CO224.csv     2 11294616    0.7995743
Light1   Light1.csv     3 12454627    0.7104398
Light24 Light24.csv     3  8668044    0.7049407
NaCl1     NaCl1.csv     4  6550232    0.7554182
NaCl24   NaCl24.csv     4 11475570    0.8774054
NaNO31   NaNO31.csv     5 10521142    1.3035997
NaNO324 NaNO324.csv     5  9045259    1.4339691
pH1         pH1.csv     6 11850666    1.0481779
pH24       pH24.csv     6  9275757    0.7866712
Temp1     Temp1.csv     7 11726477    1.2511421
Temp24   Temp24.csv     7  8120977    1.5085468
> # plotMDS(RG)
> # nrow(RG)
> Condition<- factor(c(ARef,ARef,CO2,CO2,Light,Light,NaCl,NaCl,NaNO3,NaNO3,pH,pH,Temp,Temp))
Error in factor(c(ARef, ARef, CO2, CO2, Light, Light, NaCl, NaCl, NaNO3,  : 
  object 'ARef' not found
> Time<- factor(c("1","24", "1", "24", "1", "24", "1", "24", "1", "24","1", "24", "1", "24"))
> data.frame(Sample=colnames(RG),Condition,Time)
Error in data.frame(Sample = colnames(RG), Condition, Time) : 
  object 'Condition' not found                                                                                                                      I do not understand why the object ARef is not found when currently is appearing in RG. I will appreciate any solution to this issue.

Thanks 

 

design matrix • 908 views
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The following lines are executed very well.

Condition<-factor(c("ARef","ARef","CO2","CO2","Light","Light","NaCl","NaCl","NaNO3","NaNO3","pH","pH","Temp","Temp"))

Time<- factor(c("1", "24","1", "24", "1", "24", "1", "24", "1", "24","1", "24", "1", "24"))
data.frame(Sample=colnames(RG),Condition,Time)
design <-model.matrix(~~Condition+Time)
rownames(design)<-colnames(RG)
design

----------------------------------------

Now, I would like to create the following plots:

1) The # of false discoveries vs the # of genes selected for the Fisher test (total reads) and the Fisher test (TMM)

2)  The # of false discoveries vs the # of genes selected for the Poisson-Exact and Poisson-LR-TMM normalized with my datasets.

Any helpful to perform these plots will be appreciated.

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Entering edit mode
Aaron Lun ★ 28k
@alun
Last seen 21 hours ago
The city by the bay

You need to read up on how R works. Your Condition assignment is looking for a variable named ARef, which doesn't exist in the current session. What you really want is the string "ARef", so you should be doing:

Condition <- factor(c("ARef","ARef","CO2","CO2","Light","Light",
    "NaCl","NaCl","NaNO3","NaNO3","pH","pH","Temp","Temp"))

... or even easier:

Condition <- factor(sub("(1|24)$", "", rownames(RGsamples)))

Obviously, once Condition is defined, then the second error will also be resolved.

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Thanks for your answer. Everything now works very well.

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