Question: gene expression data of scRNA-Seq
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gravatar for jabbari.parnian
10 months ago by
jabbari.parnian0 wrote:

Hi all,

I have downloaded the processed data of a scRNA-seq experiment from GEO (GSE72056). when I open the data in R, for the first column I get all the gene names instead of one gene name.

> a[1,1]
[1] tumor
23687 Levels: 1-Dec A1BG A1BG-AS1 A1CF A2M A2M-AS1 A2ML1 A2MP1 A4GALT A4GNT AA06 AAAS AACS AACSP1 AADAC AADACL2 AADACL3 AADACL4 AADAT AAED1 AAGAB AAK1 AAMDC AAMP ... ZZZ3
> a[2,1]
[1] malignant(1=no,2=yes,0=unresolved)
23687 Levels: 1-Dec A1BG A1BG-AS1 A1CF A2M A2M-AS1 A2ML1 A2MP1 A4GALT A4GNT AA06 AAAS AACS AACSP1 AADAC AADACL2 AADACL3 AADACL4 AADAT AAED1 AAGAB AAK1 AAMDC AAMP ... ZZZ3
> a[3,1]
[1] non-malignant cell type (1=T,2=B,3=Macro.4=Endo.,5=CAF;6=NK)
23687 Levels: 1-Dec A1BG A1BG-AS1 A1CF A2M A2M-AS1 A2ML1 A2MP1 A4GALT A4GNT AA06 AAAS AACS AACSP1 AADAC AADACL2 AADACL3 AADACL4 AADAT AAED1 AAGAB AAK1 AAMDC AAMP ... ZZZ3
> a[4,1]
[1] C9orf152
23687 Levels: 1-Dec A1BG A1BG-AS1 A1CF A2M A2M-AS1 A2ML1 A2MP1 A4GALT A4GNT AA06 AAAS AACS AACSP1 AADAC AADACL2 AADACL3 AADACL4 AADAT AAED1 AAGAB AAK1 AAMDC AAMP ... ZZZ3
> a[5,1]
[1] RPS11
23687 Levels: 1-Dec A1BG A1BG-AS1 A1CF A2M A2M-AS1 A2ML1 A2MP1 A4GALT A4GNT AA06 AAAS AACS AACSP1 AADAC AADACL2 AADACL3 AADACL4 AADAT AAED1 AAGAB AAK1 AAMDC AAMP ... ZZZ3
> a[1,2]
[1] 72
> a[2,2]
[1] 1
> a[1,3]
[1] 58
> dim(a)
[1] 23689  4646

I don't understand how I can find the gene expression value for gene A1BG, for example. Do you know how I can find the gene expression level for each gene?

geo scrna-seq • 219 views
ADD COMMENTlink modified 10 months ago • written 10 months ago by jabbari.parnian0

Please share the command you have used to open the file in R.

ADD REPLYlink written 10 months ago by Arup Ghosh2.8k

I used read.delim("filename")

ADD REPLYlink written 10 months ago by jabbari.parnian0

Try read.delim(file, header=TRUE, sep="\t")

ADD REPLYlink written 10 months ago by Arup Ghosh2.8k

it's still the same...

ADD REPLYlink written 10 months ago by jabbari.parnian0
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