Question

To start organising data for DESeq2

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angkoo ▴ 10

@angkoo-23537

Last seen 2.5 years ago

United Kingdom

Hi there,

I would like to ask about organising my data for DESeq2 - to do RNAseq analysis.

How do I not include my first column (gene ID) for my rawcount data as I am unable to cross check my metadata rownames with my rawcounts column names using the following command:

all(rownames(metadata) == colnames(rawcounts)) longer object length is not a multiple of shorter object length

Please help. Thanks

deseq2 • 1.3k views

ADD COMMENT • link updated 4.7 years ago by swbarnes2 ★ 1.4k • written 4.7 years ago by angkoo ▴ 10

Kevin Blighe · Answer 1 · 2020-05-16

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swbarnes2 ★ 1.4k

@swbarnes2-14086

Last seen 2 days ago

San Diego

You need to import your count data so that your gene names are row names.

ADD COMMENT • link 4.7 years ago swbarnes2 ★ 1.4k

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How do I import it the gene names as row names?

ADD REPLY • link 4.7 years ago angkoo ▴ 10

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Hey angkoo, can you tell us what is the output of the following commands?

rawcounts[1:5, 1:5]

head(metadata)

dim(rawcounts)

dim(metadata)

ADD REPLY • link 4.7 years ago Kevin Blighe ★ 4.0k

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rawcounts[1:5, 1:5]
A tibble: 5 x 5
  ERR1665724 ERR1665725 ERR1665726 ERR1665727 ERR1665728
  <dbl>      <dbl>      <dbl>      <dbl>      <dbl>
1       3494       2179       2822       2293       3548
2         38         48        107        176         23
3       1173       1171       1027        887       1170
4       1149       1123       1209        938       1247
5        330        346        319        249        362


head(metadata)
        zone condition
1 peripheral    benign
2 peripheral malignant
3 peripheral    benign
4 peripheral    benign
5 peripheral    benign
6 peripheral    benign


dim(rawcounts)
[1] 65217    18


dim(metadata)
[1] 18  2

ADD REPLY • link updated 4.7 years ago by Kevin Blighe ★ 4.0k • written 4.7 years ago by angkoo ▴ 10

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Great. Assuming that your columns in rawcounts are aligned perfectly with the rows of your metadata, all that you need to do is:

rownames(metadata) <- colnames(rawcounts)

ADD REPLY • link 4.7 years ago Kevin Blighe ★ 4.0k