Hi all, I thought finding an answer to do this would be easy but since I clearly don't know the required R code to do it, I'm here asking for help. I've generated a DESeq2 csv file containing my normalized counts organized by row (Ensembl ID's) as a R df called DSNorm. See my code below. One, I'm not sure why I'm not getting any results back from BiomaRt (0 rows)? Is it because my filter object isn't a character vector? If that's it, how can I export my DSNorm first column (my ensembl ID's) as a character vector in the filter object? Second, once I get the biomaRt part to function correctly, how can I insert the attained gene_biotypes into a new column of my DSNorm data frame (ensuring the rows align)? Any insight or suggestions would be helpful? Thanks all!

Code should be placed in three backticks as shown below

#load DESeq2
library("DESeq2")

#read in the above data
cts <- read.csv("counts_ILTK.csv", header=TRUE, row.names=1)
coldata <- read.csv("DEG_exp.csv", header=TRUE, row.names=1)
coldata <- coldata[,c("condition","type")]

# construct the Deseq2 data set
dds1 <- DESeqDataSetFromMatrix(countData=cts, colData=coldata, design=~condition, tidy=TRUE)

#calculate normalized counts and export
dds <- estimateSizeFactors(dds1)
table_counts_normalized <- counts(dds, normalized=TRUE)
write.csv(table_counts_normalized, "TKvIL_DESeq2_Counts.csv", row.names=TRUE)

#use biomaRt to get Ensembl bio types for my Genes.
DSNorm <- read.csv("TKvIL_DESeq2_Counts.csv", header=TRUE)

#assign Col1 for row names
rownames(DSNorm) <- DSNorm$ensembID
filter<-rownames(DSNorm)

#Annotate with gene biotype
library("biomaRt")

mart = useMart("ensembl","hsapiens_gene_ensembl")
getBM(attributes='gene_biotype', filters = 'ensembl_gene_id', values = filter, mart = mart)

# include your problematic code here with any corresponding output 
# please also include the results of running the following in an R session 

> getBM(attributes='gene_biotype', filters = 'ensembl_gene_id', values = filter, mart = mart)

Batch submitting query [======>-----------------------------------------------------------------------------------------]   8% eta: 10s
Batch submitting query [==============>---------------------------------------------------------------------------------]  15% eta:  9s
Batch submitting query [=====================>--------------------------------------------------------------------------]  23% eta:  8s
Batch submitting query [=============================>------------------------------------------------------------------]  31% eta:  7s
Batch submitting query [====================================>-----------------------------------------------------------]  38% eta:  6s
Batch submitting query [===========================================>----------------------------------------------------]  46% eta:  5s
Batch submitting query [===================================================>--------------------------------------------]  54% eta:  6s
Batch submitting query [==========================================================>-------------------------------------]  62% eta:  7s
Batch submitting query [=================================================================>------------------------------]  69% eta:  6s
Batch submitting query [=========================================================================>----------------------]  77% eta:  4s
Batch submitting query [================================================================================>---------------]  85% eta:  3s
Batch submitting query [========================================================================================>-------]  92% eta:  1s

[1] gene_biotype
<0 rows> (or 0-length row.names)

sessionInfo( )

You don't give enough information to go on, but two things to keep in mind.

1.) It's always best to ask to get your filters back, because biomaRt queries a relational database, and there is no expectation that the order will be preserved.

2.) You don't provide enough information for anybody to help you. What are your IDs? You need to show an example.

Here's an example of what could be going on.

> library(biomaRt)
> mart <- useEnsembl("ensembl","hsapiens_gene_ensembl")
## need some Ensembl IDs
> library(org.Hs.eg.db)

> ids <- head(keys(org.Hs.eg.db, "ENSEMBL"), 20)
> head(ids)
[1] "ENSG00000121410" "ENSG00000175899" "ENSG00000256069" "ENSG00000171428"
[5] "ENSG00000156006" "ENSG00000196136"
## Query, asking for the IDs to be returned as well
> getBM(c("ensembl_gene_id","gene_biotype"), "ensembl_gene_id", ids, mart)
   ensembl_gene_id                       gene_biotype
1  ENSG00000090861                     protein_coding
2  ENSG00000107331                     protein_coding
3  ENSG00000114771                     protein_coding
4  ENSG00000121410                     protein_coding
5  ENSG00000127837                     protein_coding
6  ENSG00000129673                     protein_coding
7  ENSG00000131269                     protein_coding
8  ENSG00000156006                     protein_coding
9  ENSG00000165029                     protein_coding
10 ENSG00000167972                     protein_coding
11 ENSG00000171428                     protein_coding
12 ENSG00000175899                     protein_coding
13 ENSG00000183044                     protein_coding
14 ENSG00000196136                     protein_coding
15 ENSG00000204574                     protein_coding
16 ENSG00000225989                     protein_coding
17 ENSG00000231129                     protein_coding
18 ENSG00000232169                     protein_coding
19 ENSG00000236149                     protein_coding
20 ENSG00000256069 transcribed_unprocessed_pseudogene

## but what if you have versioned IDs?
> z <- getBM("ensembl_gene_id_version", "ensembl_gene_id", ids, mart)
> head(z)
  ensembl_gene_id_version
1      ENSG00000090861.17
2      ENSG00000107331.18
3      ENSG00000114771.14
4      ENSG00000121410.12
5      ENSG00000127837.10
6      ENSG00000129673.10

## try using those, but don't tell biomaRt about it...
> getBM(c("ensembl_gene_id","gene_biotype"), "ensembl_gene_id", z[,1], mart)
[1] ensembl_gene_id gene_biotype   
<0 rows> (or 0-length row.names)