Question: Differential Expression Analysis : Question regarding DEseq2 Input
0
gravatar for venura
9 weeks ago by
venura10
venura10 wrote:

Hi,

I want to do a differential expression analysis using DESeq2 and I have a question regarding the input. Currently I have csv file with following information for each sample. Unfortunately, I dont have access to raw data. I am trying to figure out how to input this data. Can I straightaway use expected counts?

gene_id transcript_id(s)    length  expected_count  FPKM
AT1G01010   AT1G01010.1 1688    79  2.43

Can some one help me to go forward with my analysis? Thank you in advance. VH

rna-seq deseq2 • 212 views
ADD COMMENTlink modified 9 weeks ago • written 9 weeks ago by venura10
1

That looks like RSEM output. You can process that for DESeq2 analysis with tximport.

ADD REPLYlink written 9 weeks ago by igor8.9k

Thank you so much. I will use tximport. However, there is a problem compared to the example given there. I have individual files with count data. They have different number of rows.

  • Is there a way to input files separately or a quick way combine them based on gene names?
  • What should I do about genes missing genes (those didnt appear since there there are no counts)? Thank you!
ADD REPLYlink written 9 weeks ago by venura10
1

I don't believe tximport supports different numbers of genes in your samples; so, you could try:

  1. Read all samples into a list object
  2. Derive a unique list of gene names across all samples
  3. Using the unique list, for each sample, add extra rows (where needed) for missing genes. Fill these rows with 0 / zeros
ADD REPLYlink written 9 weeks ago by Kevin Blighe52k
1

I would be concerned about different number of rows. That suggests that the samples were quantified against different versions of the transcriptome, so there may be differences simply due to the same being gene not represented by the same sequence.

ADD REPLYlink modified 8 weeks ago • written 8 weeks ago by igor8.9k

I guess I will somehow try get raw files and do the analysis from scratch!

ADD REPLYlink written 8 weeks ago by venura10
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