Problem in running DESeq from expected count data of Transcriptome by Trinity followed by RSEM
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shashank • 0
@ac3ae973
Last seen 10 months ago
Israel

Hi; I am trying to analyse tissue specific expression and fold change by DESeq2 for Denovo assembelled transcriptome Problem is that I have a data matrix file of Expected counts in which some values are decimal So I am trying to convert them into integer by round() but I am getting Error code and error below

> data <- round(data)
Error in Math.data.frame(list(TranscriptID = c("TRINITY_DN61711_c0_g1_i1",  : 
  non-numeric-alike variable(s) in data frame: TranscriptID

Can Anyone help me in changing all the values to integer without effecting my 1st column which is basically header of each row in my data

Or If there is some better pipeline to follow....

Thanks Shashank

Tissue Spati RSEM deno DEseq2 • 831 views
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Basti ▴ 750
@7d45153c
Last seen 8 days ago
France

It is more a R programming issue than a Bioconductor package issue. A quick google search would have helped you : https://stackoverflow.com/questions/9063889/how-to-round-a-data-frame-in-r-that-contains-some-character-variables

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Thanks Basti for help

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@8856e43a
Last seen 9 months ago
Vietnam

Our current system for identifying differentially expressed transcripts relies on using the EdgeR Bioconductor package. https://support.bioconductor.org/ https://candy-crush.io /

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