Question: Error in lmfit : row dimension of design doesn't match column dimension of data object
0
gravatar for muhammadzubair777
3.6 years ago by
muhammadzubair77710 wrote:

anyone can help to resolve this issue.

> fit = lmFit(gse28403eset,design_gse28403) 

>Error in lmFit(gse28403eset, design_gse28403) : 
  row dimension of design doesn't match column dimension of data object

> dim(gse28403eset)
[1] 20425    13

> dim(design_gse28403)
[1] 12  2

how can this error can be removed. any answer will be appreciated. thank you.

ADD COMMENTlink modified 3.6 years ago by genomax91k • written 3.6 years ago by muhammadzubair77710
0
gravatar for Santosh Anand
3.6 years ago by
Santosh Anand5.2k
Santosh Anand5.2k wrote:

The error message is very clear. The design has 12 rows, while the data (eset) has 13 columns. They should exactly match. You are missing either one row in design or have an extra col in data.

ADD COMMENTlink written 3.6 years ago by Santosh Anand5.2k

sir how can i adjust this. i have tried alot to resolve this issue but cann't find the solution. i am using following commands

groups = pData(phenoData(gse28403dat[[1]]))$characteristics_ch1

groups=as.character(groups)

groups[groups=="disease state: Castration-resistant prostate cancer"]="castration"

groups[groups=="disease state: Advanced prostate cancer"]="PC"

f = factor(groups, levels=c("castration","PC"))

design_gse28403 = model.matrix(~0+f)

colnames(design_gse28403) = levels(f)

cont.matrix = makeContrasts(PC-castration, levels=design_gse28403)

ADD REPLYlink modified 3.6 years ago • written 3.6 years ago by muhammadzubair77710
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