Question: Fold Change with DESeq2
0
gravatar for tweiskittel94
7 months ago by
tweiskittel940 wrote:

I have a very simple matrix of pairs of columns showing tumor RNAseq raw counts and normal tissue raw counts and rows with Ensembl IDs. I am trying to use the DESeq2 to get fold change between tumor and normal tissue. All of the DESeq tutorials or examples have much more complicated matrices with data that is structured completely differently. Does anyone have an idea of how I can use DESeq2 to get fold change from my simple matrix?

rna-seq deseq2 R • 304 views
ADD COMMENTlink written 7 months ago by tweiskittel940
1

Please show head(your.matrix, n=10)

ADD REPLYlink written 7 months ago by ATpoint13k
TCGA-E9-A3QA-01A-61R-A22K-07 TCGA-EW-A1P6-01A-11R-A144-07
ENSG00000000003                         2467                         2692
ENSG00000000005                            3                            4
ENSG00000000419                         2513                         1209
ENSG00000000457                          845                          935
ENSG00000000460                          465                          308
ENSG00000000938                         2153                          126
ENSG00000000971                         2357                         1551
ENSG00000001036                         4647                         2152
ENSG00000001084                         2635                         1570
ENSG00000001167                         4529                         2649
ADD REPLYlink modified 7 months ago by WouterDeCoster36k • written 7 months ago by tweiskittel940

there are several more columns, but that is the first pair with TCGA-E9-A3QA-01A-61R-A22K-07 being tumor and TCGA-EW-A1P6-01A-11R-A144-07 being tissue normal

ADD REPLYlink modified 7 months ago • written 7 months ago by tweiskittel940

I added markup to your post for increased readability. You can do this by selecting the text and clicking the 101010 button. When you compose or edit a post that button is in your toolbar, see image below:

101010 Button

ADD REPLYlink written 7 months ago by WouterDeCoster36k

Looks like a normal count matrix to me. What do you think is "much more complicated" in the examples you have seen? Please give a link to it.

ADD REPLYlink written 7 months ago by ATpoint13k
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