RNA sequence analyzing data using R after DESeq2 (illumina)

Question

[Bioinformatics1]

Hello,

I aligned 3 group data and used DESeq2 in https://basespace.illumina.com/analyses/

Now I excel file of data after DESeq2.

Can you guide how to continue in R and draw a plot Heatmap, and other graphs for the study of gene expression of 3 groups?

1. How do I upload excel with the below information in R?
2. When I use dds, there is an error. How I can remove the error? Thanks in advance

dds <- DESeq(dds)
Error in is(object, "DESeqDataSet") : object 'dds' not found

 baseMean log2FoldChange     lfcSE    pvalue      padj
##              <numeric>      <numeric> <numeric> <numeric> <numeric>
## FBgn0000008   95.14429     0.00119920  0.151897 0.9918817  0.997211
## FBgn0000014    1.05652    -0.00473412  0.205468 0.8172987        NA

[swbarnes2]

I strongly recommend that you set your data aside and find a DESeq2 tutorial, and run through that before looking at your data. This board is not meant to teach rudimentary R.

[Lila M]

Please, try to format your code using the appropriate tool when you write. Also is a good practice to share the code you run and how your data looks like. But as @swbarnes said, try to use a DESeq2 tutorial, here you have one. Your input should be a count table with expression values. That can be create with so many different tools, one of my favorite is featureCounts.

[Bioinformatics1]

My samples do not have replicate and receive this error: how to change the command that shows each sample has only one and there is no replication? thanks in advance

> **dds <- DESeqDataSetFromMatrix(countData=countData,
+ colData=metaData,
+ design=~dex, tidy = TRUE)**
  Note: levels of factors in the design contain characters other than
  letters, numbers, '_' and '.'. It is recommended (but not required) to use
  only letters, numbers, and delimiters '_' or '.', as these are safe characters
  for column names in R. [This is a message, not a warning or an error]
Warning message:
In DESeqDataSet(se, design = design, ignoreRank) :
  some variables in design formula are characters, converting to factors
**> dds**
class: DESeqDataSet 
dim: 26364 3 
metadata(1): version
assays(1): counts
rownames(26364): DDX11L1 WASH7P ... GOLGA2P3Y GOLGA2P2Y
rowData names(0):
colnames(3): You001STD You002Cin You003Met
colData names(4): id dex Cell.Type Geo.id
**> dds <- DESeq(dds)**
estimating size factors
  Note: levels of factors in the design contain characters other than
  letters, numbers, '_' and '.'. It is recommended (but not required) to use
  only letters, numbers, and delimiters '_' or '.', as these are safe characters
  for column names in R. [This is a message, not a warning or an error]
estimating dispersions
Error in checkForExperimentalReplicates(object, modelMatrix) : 

  The design matrix has the same number of samples and coefficients to fit,
  so estimation of dispersion is not possible. Treating samples
  as replicates was deprecated in v1.20 and no longer supported since v1.22.

[GenoMax]

Please use ADD REPLY when responding to existing posts to keep threads logically organized. SUBMIT ANSWER is only for new answers to original question.

[swbarnes2]

If you don't have replicates you can't use DESeq2.