DEG Analysis in R

Question

[anasjamshed]

I want to identify DEGs from 79 samples of GSE75693 selected based on the threshold P < 0.01 and fold change >2.0.

But my code showing following error :

Error in getEAWP(object) : data object isn't of a recognized data class

Code :

gset <- getGEO("GSE75693", GSEMatrix =TRUE, getGPL=FALSE)

gr<-c(rep("Tumor",3),("Normal"),rep("Tumor",7),("Normal"),rep("Tumor",21),rep("Normal",4) + ,rep("Tumor",5),("Normal"),rep("Tumor",17),rep("Normal",2),("Tumor"),("Normal"),rep("Tumor",2), + ("Normal"),("Tumor"))

gr<-factor(gr)

gset$description<-gr

design<-model.matrix(~description+0,gset)

colnames(design)<-levels(gr)

levels(gr)

fit<-lmFit(gset,design)

I also want to know how i can i design contrast matrix?

Answer 1

[Gordon Smyth]

getGEO returns a list of ExpressionSets rather than a simpleExpressionSet, so to pass the data to limma you need to access the relevant component by

fit <- lmFit(gset$GSE75693, design)

However your design matrix is difficult to understand. The GEO dataset you've read is not a cancer dataset so there are no tumor samples. As you have noted yourself (DEGS Analysis in R ), it is a kidney transplant dataset. You seem to have copied the design matrix from a completely different dataset (What this error means?Error in getEAWP(object) : data object isn't of a recognized data class ).

If you want to repeat the analysis from the paper you mentioned before (DEGS Analysis in R) then you need to follow what they said they did:

The dataset GSE75693 was deposited by Sigdel et al containing information of renal bioptic tissues from 30 stable renal allografts, 15 acute rejection patients, 15 BKVN patients and 12 chronic allograft nephropathy patients. Here, we selected the 30 stable renal allografts and the 15 BKVN patients as study subjects.

It is apparent that they did a two group comparison between BKVN and the stable allografts.

[anasjamshed]

thanks brother but when i try to run fit <- lmFit(gset$GSE75693, design)

it gives me the following error : Error in array(x, c(length(x), 1L), if (!is.null(names(x))) list(names(x), : 'data' must be of a vector type, was 'NULL'

[Gordon Smyth]

That error could only occur if the data object (the first argument of lmFit) was NULL, which could not be the case if you have run the code you claim to have run.

[anasjamshed]

brother plz help me. I want to identify DEGs from 79 samples of GSE75693 selected based on the threshold P < 0.01 and fold change >2.0.

Answer 2

[ES.67]

does this help ?

What this error means?Error in getEAWP(object) : data object isn't of a recognized data class

[anasjamshed]

no brother I also tried this before posting

[kamiljaron]

You know that about half of the community here are "sisters", not "brothers"? Please, use inclusive language.

[anasjamshed]

yes but I am talking with ES.67 in commnet