Why names() returns empty?

Question

[zizigolu]

Hi,

I have this data

> head(datExpr[,1:4])
            CD109  KAT5  WWC2 CD163
Control_D0   1.94 53.18 13.27  0.00
Control_D1   1.99 53.08 12.87  0.00
Control_D10  1.79 50.95 10.76  0.33
Control_D11  1.97 48.13  7.85  0.48
Control_D12  1.94 53.30  9.16  0.56
Control_D13  2.03 52.35  7.15  0.64
> names(datExpr)
NULL

probes = names(datExpr)

gives NULL (empty) values

I can't figure out why names() returns empty. Can one help me please? Thank you

[ATpoint]

Strange indeed. Did you try with rownames() and colnames()?

[zizigolu]

Thanks, my genes are in columns that I suppose should go to names

[Ram]

Maybe the names() function is overwritten in the current namespace? Does R allow that? Can you check for it?

[GenoMax]

R allows that (and here) so that must be the case here.

[zizigolu]

https://ibb.co/hG4Mnn

[ATpoint]

Good point. Try base::names() then.

[zizigolu]

> base::names() 
Error in base::names() : 0 arguments passed to 'names' which requires 1
>

[Ram]

base::names(datExpr), not just base::names() :-)

[zizigolu]

Thank you,

> base::names(datExpr)
NULL
>

Sorry, instead of names (probes = names(datExpr) ) , how can I put my genes from columns in datExpr in prob???

I did so instead: colnames(datExpr)=prob

[Ram]

base::names() gave you NULL as well? My recommendation is wrong then, your names has not been overwritten.

[zizigolu]

Yes, gave NULL. However thanks for your time

[zizigolu]

Thanks

> names()
Error in names() : 0 arguments passed to 'names' which requires 1
>

Answer 1

[jomo018]

Make sure datExpr is a data frame rather than matrix which will respond with NULL. E.g. check: names(data.frame(datExpr))

[zizigolu]

names(data.frame(datExpr)) returned my genes thanks

[zizigolu]

Sorry, in

out <- data.frame(EBDERes$PPMat[names(GeneFC$PostFC),]) 
out$FC <- GeneFC$PostFC

Am I correct that with or without out$FC <- GeneFC$PostFC the out is the same???

I mean, if I want to write out as a table, would the out change if I use out$FC <- GeneFC$PostFC code afterward????

Thank you