Question: Negative values HTSeq2
0
gravatar for rhasanvandj
5 weeks ago by
rhasanvandj10
rhasanvandj10 wrote:

Hi friends I have HTSeq data that is Log2 (X+1), I revert them to original data in excel this way: X^2=y and then the y-1=original values. Is this correct? In the resulted values I have negative values that DESeq2 cannot deal with them. what should I do with negative values if my revert approach is correct?

rna-seq • 152 views
ADD COMMENTlink modified 4 days ago by Biostar ♦♦ 20 • written 5 weeks ago by rhasanvandj10

do not transform you data for DESeq2, it expects raw count data

ADD REPLYlink written 5 weeks ago by grant.hovhannisyan2.0k

yes I know that for DESeq2 I need raw data. that is the reason I revert the log2+1 . because HTSeq data are log2+1 data not original reads. now I dont know how to deal with negative values resulted there

ADD REPLYlink written 5 weeks ago by rhasanvandj10

Please load the matrix into R and then do the un-logging. Excel might mess up things here. It is not recommended to use Excel, not reproducible and might introduce artifacts. In R:

2^matrix-1
ADD REPLYlink modified 5 weeks ago • written 5 weeks ago by ATpoint40k

Hi thanks I am new to R. Can you please explain more? By matrix you mean my data file? How should I do this exactly?

ADD REPLYlink written 5 weeks ago by rhasanvandj10

You may want to go through a basic R tutorial. If you plan on using DESeq2, you'll need to know some basics like what the different data types are and how to read/write files.

ADD REPLYlink written 5 weeks ago by igor11k
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