Error of Groups in R
0
0
Entering edit mode
6.3 years ago
12021560-040 ▴ 70
> fit = lmFit(gse50397eset, design_gse50397)

Error in lmFit(gse50397eset, design_gse50397) :
row dimension of design doesn't match column dimension of data object.


affy limma oligo bioconductor R • 2.1k views
1
Entering edit mode

Can you check and post:

dim(gse50397eset)
dim(design_gse50397)

1
Entering edit mode

dim(gse50397eset) [1] 33297 89 dim(design_gse50397) [1] 77 2 I run these commands but did not find anything useful.. :(

1
Entering edit mode

dim(gse50397eset) [1] 33297 89 dim(design_gse50397) [1] 77 2 I run these commands but did not find anything useful.. :(

1
Entering edit mode

dim tells you the sizes of your objects. And indeed, these do not match. You should check if you properly created those objects.

1
Entering edit mode

which objects aren't created properly?? and how can I make them proper match?

1
Entering edit mode

You should have a look at this thread: Error in R Script something rather similar is discussed there

1
Entering edit mode

please tell according to my script that which objects are not properly defined?

1
Entering edit mode

shouldn't this be fit = lm(gse50397eset, design_gse50397)?

Then you get fit$fitted.values ADD REPLY 1 Entering edit mode lmFit does exist (limma) ADD REPLY 1 Entering edit mode Please help me and pinpoint the error specifically If you can I am not getting any help from the above responses.. Please help me get out of this error i will be very thankful to you. gse50397dat = getGEO('GSE50397') gse50397raw= getGEOSuppFiles("GSE50397") tarfile <- grep("\\.tar$", rownames(gse50397raw), value = TRUE)
list.files("GSE50397")
untar("GSE50397/GSE50397_RAW.tar", exdir = "GSE50397/CEL")
list.files("GSE50397/CEL")
celfiles <- list.files("GSE50397/CEL", full = TRUE)
rawData
normData <- rma(rawData)
gse50397eset= exprs(normData)
groups = pData(phenoData(gse50397dat[[1]]))\$Hba1c
groups=as.character(groups)
groups=sort(groups)
groups[c(11)]="diabetic"
groups[c(17)]="diabetic"
groups[c(25)]="diabetic"
groups[c(27)]="diabetic"
groups[c(29)]="diabetic"
groups[c(32)]="diabetic"
groups[c(35)]="diabetic"
groups[c(38)]="diabetic"
groups[c(42:43)]="diabetic"
groups[c(46)]="diabetic"
groups[c(48)]="diabetic"
groups[c(51)]="diabetic"
groups[c(53:56)]="diabetic"
groups[c(61)]="diabetic"
groups[c(65)]="diabetic"
groups[c(76:78)]="diabetic"
groups[c(82:84)]="diabetic"
groups[c(87)]="diabetic"
groups[c(13:16)]="control"
groups[c(23:24)]="control"
groups[c(30:31)]="control"
groups[c(57:60)]="control"
groups[c(62:64)]="control"
groups[c(66:75)]="control"
groups[c(80:81)]="control"
groups[c(88:89)]="control"
f = factor(groups, levels=c("control","diabetic"))
design_gse50397 = model.matrix(~0+f)
colnames(design_gse50397) = levels(f)
cont.matrix = makeContrasts(T2D-diabetic, levels=design_gse50397)
fit = lmFit(gse50397eset, design_gse50397)
Error in lmFit(gse50397eset, design_gse50397) :
row dimension of design doesn't match column dimension of data object

1
Entering edit mode

What an absurd way of creating your trait data object, I would like to suggest you first follow a proper introduction to R before you try to do research. I'd suggest http://swirlstats.com/