Error in R Script

Question

[786]

Hi I was retrieving differentially expressed genes through R and got an error at the very last step. Please help me out in removing following error it will be very helpful.

Error
results= topTable(fit2, adjust ='BH', number = nrow(gse32269eset))
Error in (function (..., row.names = NULL, check.rows = FALSE, check.names = TRUE, :
arguments imply differing number of rows: 54675, 22283

[Shamim Sarhadi]

I think It's related to selecting the number of DEGs,why you select all the prob-id in your GSE? try with a number,lets say 100, I suggest you specify log fold change for your topranked gene e.g logFC=0.05

Answer 1

[ATRX]

try using: topTable(fit2, adjust ='BH', number = Inf)

I think you are filtering some probes or aggregating the probes due to which there is a difference in the number of rows between fit2 and nrow(gse32269eset)

[786]

I got the same error by running this command..Can you please help me more?

[ATRX]

I am not sure but it is working for me. I presume that you are using GSE32269

> exprs = exprs(eset) 
> dim(exprs)
[1] 22283    55
> design <- model.matrix(~ type + Tmprss2.erg + 0, as.data.frame(group))
> head(design)
  typePrimary typeMet typeNormal Tmprss2.ergPositive
1           1       0          0                   0
2           1       0          0                   0
3           1       0          0                   0
4           1       0          0                   0
5           1       0          0                   0
6           1       0          0                   0
> cont.matrix <- makeContrasts(NormalvsPrimary = typePrimary-typeNormal, levels=design)
> print(cont.matrix)
                     Contrasts
Levels                NormalvsPrimary
  typePrimary                       1
  typeMet                           0
  typeNormal                       -1
  Tmprss2.ergPositive               0
> fit1 <- lmFit(exprs, design)
> fit2 <- contrasts.fit(fit1, cont.matrix)
> fit2 <- eBayes(fit2)
> results <- topTable(fit2, "NormalvsPrimary", number=Inf)
> head(results)
                logFC   AveExpr         t      P.Value    adj.P.Val        B
201596_x_at  6.359687 10.604378  18.36430 9.175354e-25 2.044544e-20 45.75283
215054_at   -1.735632  5.432611 -17.25748 1.593483e-23 1.775379e-19 43.02282
211820_x_at -2.799107  4.629426 -16.60052 9.224250e-23 6.374164e-19 41.33593
206207_at   -4.621926  6.161970 -16.52111 1.144220e-22 6.374164e-19 41.12856
206676_at   -5.027171  4.179033 -16.01332 4.615017e-22 2.056728e-18 39.78449
204959_at   -5.102275  4.839911 -15.76017 9.351825e-22 3.473112e-18 39.10262

[786]

It worked but I need gene names too in my results how can I get them??

[ATRX]

You need annotation file from Affymetrix and then map it to the probes. You may also use David to convert them to gene ids/gene symbol.

[786]

Thank u so much for our help.

[Shamim Sarhadi]

https://biodbnet-abcc.ncifcrf.gov/db/db2db.php is a nice tool to convert prob-id to gene symbol

[786]

Thanx alot fr your help.

[zizigolu]

Sorry I have ovary cancer samples stage 1, 2, 3 and normal samples I was going to have something like your above code resulted in P.value , adj.P.Val , logFC

I did like below

library(limma)

library(affy)

Data<-ReadAffy()

eset<-rma(Data)

exprs<-exprs(eset)

dim(exprs)

[1] 54675 4

design <- model.matrix(~ type + Tmprss2.erg + 0, as.data.frame(group))

Error in as.data.frame(group) : object 'group' not found

Actually I was going to compare normal with rest of cancers in 3 stages but I got error

how I can have your top table please?

[ATRX]

Com'on.. you need to define the group first.. i.e. which sample belongs to which group. Read about limma first and try to understand the code. Please think and apply. I am sure you don't want yourself to be spoon-fed.

[GenoMax]

It is never a good idea to ask a new unrelated question in an existing thread. Please start a new thread.

[zizigolu]

Sorry If I ask such a question in a new thread the Admins will close my post abruptly because they supposed me as a spoon-feed OP :)