Question: constructing a DESeqDataSet
0
gravatar for linouhao
18 months ago by
linouhao0
linouhao0 wrote:

2017xmq

19 分钟前

the function DESeqDataSetFromMatrix can be used if you already have a matrix of read counts prepared from another source; If you have transcript quantification files, as produced by Salmon, Sailfish, or kallisto, you would use DESeqDataSetFromTximport.

but i always see DESeqDataSetFromMatrix is the most used in tutorial, what is the detailed difference? thanks in advance

deseq2 deseqdataset • 251 views
ADD COMMENTlink modified 18 months ago by Michael Love26k • written 18 months ago by linouhao0

As far as I understood, DESeqDataSetFromTximport has the same purpose that DESeqDataSetFromMatrix but it can directly accept the output of a psedoaligner such as Salmon, producing directly the count matrix.

With DESeqDataSetFromMatrix, you need to have a count matrix already prepared with genes as rows ans samples as columns.

Hope this help

ADD REPLYlink modified 18 months ago • written 18 months ago by Aurora10
Answer: constructing a DESeqDataSet
0
gravatar for Michael Love
18 months ago by
Michael Love26k
United States
Michael Love26k wrote:

Please see the help files for these functions:

?DESeqDataSet

The help files are where we put details about functions.

ADD COMMENTlink written 18 months ago by Michael Love26k
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