Hi,

I am working with isoforms.results from RSEM analysis.

I am trying to annotate my deseq results with symbol and entrez IDs, following the vignette http://master.bioconductor.org/packages/release/workflows/vignettes/rnaseqGene/inst/doc/rnaseqGene.html#annotating-and-exporting-results

Unfortunately, I cannot export them as a csv file because the 2 elements I am adding are list.

do you have any idea how this is happening? Below the code I am using.

Please, let me know if you need further information.

Thank you

res <- results(dds, contrast=c("treatment","drug","vehicle"), tidy=TRUE)    

> head(res)
                    row   baseMean log2FoldChange      lfcSE       stat     pvalue      padj
1  ENSMUST00000000001.5 508.710745    -0.01199816 0.08030722 -0.1494033 0.88123544 0.9941563
2 ENSMUST00000000003.14   0.000000             NA         NA         NA         NA        NA
3  ENSMUST00000114041.3   0.000000             NA         NA         NA         NA        NA
4 ENSMUST00000000028.14  53.297655    -0.12999380 0.23479087 -0.5536578 0.57981305 0.9560011
5 ENSMUST00000096990.10   8.682780     2.34835304 1.86921663  1.2563301 0.20899633 0.7698453


#create a new column with ensembl_gene_id 

library(biomaRt)
library(org.Mm.eg.db)
library(dplyr)
library("AnnotationDbi")
library(tidyverse)
ensembl=useMart("ENSEMBL_MART_ENSEMBL")
ensembl <- useDataset("mmusculus_gene_ensembl", mart = ensemble)


filterType <- "ensembl_transcript_id_version"
filterValues <- res$row
attributeNames <- c("ensembl_transcript_id_version", "ensembl_gene_id")

annot <- getBM(attributes=attributeNames,
               filters = filterType,
               values = filterValues,
               mart = ensemble) 

names(annot) <- c("row", "ensembl_gene_id")

res <- merge(res, annot, all.x=TRUE)

#Annotating symbol and entrez IDs with mapIds

res$symbol <- mapIds(org.Mm.eg.db,
                     keys=res$ensembl_gene_id,
                     column="SYMBOL",
                     keytype="ENSEMBL",
                     multiVals="first")

res$entrez <- mapIds(org.Mm.eg.db,
                       keys=res$ensembl_gene_id,
                       column="ENTREZID",
                       keytype="ENSEMBL",
                       multiVals="first")

 > head(res_1)
                    row   baseMean log2FoldChange      lfcSE       stat      pvalue       padj    ensembl_gene_id symbol entrez
1  ENSMUST00000000001.5 508.710745    -0.01199816 0.08030722 -0.1494033 0.881235438 0.99415633 ENSMUSG00000000001  Gnai3  14679
2 ENSMUST00000000003.14   0.000000             NA         NA         NA          NA         NA ENSMUSG00000000003   Pbsn  54192
3  ENSMUST00000000010.9  11.241632    -0.90230395 0.79248598 -1.1385740 0.254880870 0.81279086 ENSMUSG00000020875  Hoxb9  15417
4 ENSMUST00000000028.14  53.297655    -0.12999380 0.23479087 -0.5536578 0.579813045 0.95600111 ENSMUSG00000000028  Cdc45  12544
5 ENSMUST00000000033.12 344.732181    -0.42331235 0.13223803 -3.2011394 0.001368853 0.05267212 ENSMUSG00000048583   Igf2  16002



res <- as.data.frame(res)
write.csv(res, file = "results.csv")

# > write.csv(res, file = "results.csv")
Error in utils::write.table(res, file = "results.csv", col.names = NA,  : 
  unimplemented type 'list' in 'EncodeElement

Note that a data.frame is actually a list object, and a list can have another list as an element.

> d.f <- data.frame(this = letters, that = LETTERS)
> d.f$theother <- as.list(letters)
> d.f
   this that theother
1     a    A        a
2     b    B        b
3     c    C        c
4     d    D        d
5     e    E        e
6     f    F        f
7     g    G        g
8     h    H        h
9     i    I        i
10    j    J        j
11    k    K        k
12    l    L        l
13    m    M        m
14    n    N        n
15    o    O        o
16    p    P        p
17    q    Q        q
18    r    R        r
19    s    S        s
20    t    T        t
21    u    U        u
22    v    V        v
23    w    W        w
24    x    X        x
25    y    Y        y
26    z    Z        z
> write.csv(d.f, "fakeo.csv")
Error in utils::write.table(d.f, "fakeo.csv", col.names = NA, sep = ",",  : 
  unimplemented type 'list' in 'EncodeElement'

You could do sapply(res, class) to figure out which elements are list, and then deal with that as you see fit.