Error in `[.data.frame`(pData(eset), , symLabel) : undefined columns selected
2
0
Entering edit mode
6.5 years ago

i followed this script in R

>library(inSilicoMerging)

>library("inSilicoDb")

>InSilicoLogin("username", "password")

>eset1 = getDataset("GSE5847","GPL96",norm= "ORIGINAL", features = "PROBE", curation = 5159)

>eset2 = getDataset("GSE20685","GPL570", norm="ORIGINAL", features = "PROBE", curation = 18031)

>esets = list(eset1,eset2)

>plotMDS(eset_FRMA,colLabel="Disease",symLabel="Study",main="FRMA (No Transformation)")

 

and then R show me this error:

Error in `[.data.frame`(pData(eset), , symLabel) : 
  undefined columns selected

how can i solve this error???

 

R • 6.2k views
ADD COMMENT
1
Entering edit mode
6.5 years ago
michael.ante ★ 3.7k

It seems you missed

eset_FRMA = merge(esets);

from code chunk #3

ADD COMMENT
0
Entering edit mode

tnx michael 

but affter adding 

eset_FRMA = merge(esets);

I'm getting the same error again !!!!

ADD REPLY
1
Entering edit mode

You could have a look at the pData of the data sets (see ?plotMDS):

 # check available annotations:
     colnames(pData(eset_FRMA))
     table(pData(eset_FRMA)[,"Disease"]);
     table(pData(eset_FRMA)[,"Study"]);

Maybe the names differ and could therefore not be merged correctly...

If the error still persists, contact the authors of the package directly.

ADD REPLY
0
Entering edit mode

hi Michael, i am getting the same error.

ADD REPLY
1
Entering edit mode

Hi 1234anjalianjali1234 that problem was related to clinical data that comes with expression data

check your clinical data, you should know, even if the clinical data and your plot lables(sym or col lable)have difference in one letter it'll give you the same error, also it sensitive to capital or lower case letter in your pData(like my case)

ADD REPLY
0
Entering edit mode

Thanks for the help, it worked. But now I am facing another problem. while validating the data I am getting new error.

> plotGeneWiseDensity(eset_NONE,
+ batchAnnot = "Study",
+ gene = "MMP2",
+ main = "NONE (No Transformation)");

Error: could not find function "plotGeneWiseDensity"

> plotDendrogram(eset_NONE,
+ batchAnnot = "Study",
+ main = "NONE (No Transformation)",
+ legend = FALSE);

Error: could not find function "plotDendrogram"

> plotGeneWiseBoxPlot(eset_NONE,
+ batchLabel = "Study",
+ colLabel = "X.Sample_characteristics_ch1",
+ gene = gene,
+ main = "NONE (No Transformation)");

Error in exprs(eset)[gene, idx] : subscript out of bounds

it would be great if you can help.

ADD REPLY
0
Entering edit mode
5.5 years ago

Actually as far as I know insilicomerging package does not support plotGeneWiseDensity and plotDendrogram anymore in the latest version, you could ask insilicodb admin for more information

ADD COMMENT
0
Entering edit mode

@Shamim Sarhadi it shows in the error message that getDataset does not exist as a function in the inSilicoMerging package. I suggest you make a small example of your data and then tell what you want to do, so people could help you easier

ADD REPLY
0
Entering edit mode

@Mo, getDataset is a function in insilicoDB package.

ADD REPLY

Login before adding your answer.

Traffic: 1909 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6