Question

DESeq2 Normalisation out of excel data?

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mueslirapper • 0

@mueslirapper-22776

Last seen 5.8 years ago

Is it possible to do a DESeq2 in R out of a .xlsx data? If not, which kind of format do i need? my data is available in the following matrix:

                 gen   a...   b..  b...

patient
1.. counted reads 2... counted reads 3... counted reads

thanks for any kind of help!

deseq2 • 2.0k views

ADD COMMENT • link 5.8 years ago mueslirapper • 0

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thank you for that advice, but i could`t use that script well, because my data are different...

My data is a gene expression analysis in which the frequency of 549 different genes was measured in 24 test persons... i.e. independent raw data (counts)

is it even possible to make a DeSeq2-normalisation with this data?

when i summarized my data it shows up like this (:

SummarizedExperiment(c) class: SummarizedExperiment dim: 24 549 metadata(0): assays(1): '' rownames(24): 1 2 ... 23 24 rowData names(0): colnames(549): ACTB ATP5F1 ... XCL2 XCR1 colData names(0):

ADD REPLY • link 5.8 years ago mueslirapper • 0

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You will need to collaborate with a bioinformatician or someone familiar with R/Bioconductor. It should be straightforward to take the approach I outlined below, exporting CSV and importing using the information in the count matrix input section.

The support site is for specific questions about software, but here you just need to closely read the vignette or the workflow, or instead work with someone who can help out with loading the data into R.

ADD REPLY • link 5.8 years ago Michael Love 43k

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because i have 0 colData names...

ADD REPLY • link 5.8 years ago mueslirapper • 0

score 0 · Answer 1 · 2020-01-27

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Michael Love 43k

@mikelove

Last seen 5 days ago

United States

Please consult the software vignette and/or the workflow (linked from the beginning of the vignette).

ADD COMMENT • link 5.8 years ago Michael Love 43k

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i want to follow that script: https://bioc.ism.ac.jp/packages/2.14/bioc/vignettes/DESeq2/inst/doc/beginner.pdf

but i only have a xlxc data...and no BAM.file

ADD REPLY • link 5.8 years ago mueslirapper • 0

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That's a very old vignette (2014).

Start by going to https://bioconductor.org/packages/DESeq2

Then click on the HTML link under Documentation, and read the section "Count matrix input".

It will be up to you to output counts from Excel and read them into R (easiest is export CSV => read.csv or readr::read_csv), if you are stuck at this step you will need to collaborate with someone who has a little R experience, or try to learn about basics of reading in data into R.

ADD REPLY • link 5.8 years ago Michael Love 43k