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convert raw microarray expression values to TPM

Hi everyone,

I'm trying to create a scatterplot of expression values of the differentially expressed gene I found by microarray differential expression analysis between two distinct tumour types (WDLPS and DDLPS).

However, before I do this does anyone know if I should convert the raw expression values to TPM. If so, how might I do this? Also how do I find out the length of this gene for TPM?

Please find below a table of expression values for the selected gene.

 head(df)
        Samples Expression.value Tumour.type
1 GSM766533.CEL        10.013128       DDLPS
2 GSM766534.CEL         9.293059       DDLPS
3 GSM766535.CEL        10.821439       DDLPS
4 GSM766536.CEL        10.494755       DDLPS
5 GSM766537.CEL        10.736248       DDLPS
6 GSM766538.CEL        10.067121       DDLPS

Thankyou

microarray tpm scatterplot
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written by bioinformatics • bioinformatics

1 answer

It’s an array. The concept of counts and length does not apply. Use the values you have which sre already log2 scale. Pro-tip: Use existing plotting functions everyone uses if you struggle writing code yourself. glimma for example has many visualization options.

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written by ATpoint ATpoint

Ok thanks for your help. I will use the expression values from the table.

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written by bioinformatics • bioinformatics

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