Question

DESeq2 Following RSEM

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tungphannv ▴ 10

@tungphannv-12640

Last seen 7.8 years ago

I am using RNA-seq data processed by RSEM given by someone else. The data has this format:

         sample1 sample2 sample3 sample4 sample5 sample6
A1BG       94.64  278.03   94.07   96.00   55.00   64.03
A1BG-AS1   64.28  114.08   98.88  109.05   95.32   73.11
A1CF        0.00    2.00    1.00    1.00    0.00    1.00
A2M        24.00    2.00   18.00    4.00   35.00    8.00
A2M-AS1     1.00    1.00    1.00    0.00    0.00    0.00
A2ML1       0.84    2.89    0.00    1.00    2.00    3.11

But seems like DESeq2 can't handle integers. I tried tximport but hasn't been able to implement it for it to work, also I don't understand how/whether tximport would help in this situation. Can I just use round(data) instead? Anyone has better suggestion to deal with this kind of data? Thanks so much!

deseq2 rnaseq • 11k views

ADD COMMENT • link updated 7.8 years ago by Michael Love 43k • written 7.8 years ago by tungphannv ▴ 10

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The DESeq2 manuals says: "As input, the DESeq2 package expects count data as obtained", which means just handles whole numbers. I doubt that "round" is a good approach here, because you change the counts. Where does the e.g. 0.64 count from Sample1 A1BG come from?

ADD REPLY • link 7.8 years ago Walter F. Baumann ▴ 10

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I think it comes from the way RSEM assign their counts to certain genes since RSEM estimates abundances for transcript/genes.

ADD REPLY • link 7.8 years ago tungphannv ▴ 10

score 2 · Answer 1 · 2017-03-20

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Michael Love 43k

@mikelove

Last seen 1 hour ago

United States

hi,

Use tximport to import the RSEM estimated counts. This will take care of everything for you. If you encounter a problem, please report back with full documentation of your code and the error and your sessionInfo().

There is an example in the tximport vignette of importing RSEM estimated counts.

ADD COMMENT • link 7.8 years ago Michael Love 43k

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From the vignette, I think tximport expect a list of .genes.files from RSEM. For some reason, I don't have those files. The only data I have is the tsv file with the expected counts in above format (e.g first column is the list of genes, and the next 8 columns contains expected counts - 4 of them are control).

Is it possible to make it work with tximport/deseq2 ? Thank you very much.

ADD REPLY • link 7.8 years ago tungphannv ▴ 10

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So this is a little sub-optimal compared to using tximport (which leverages the effective length information and isoform abundance estimates), but you can round the matrix of estimated counts (note, these are not normalized counts) and feed these into DESeqDataSetFromMatrix.

ADD REPLY • link 7.8 years ago Michael Love 43k