Comments (1)
If you have follow up questions, let's continue on the support site, as this is where most people go to look for tximport usage questions.
"the way to go is ... the estimated counts...with the edgeR pipeline described in the tximport vignette"
Yes, the default recommendation is to import estimated counts and use the gene lengths as a per-sample offset. This is what happens if you use the DESeq2 or edgeR code in the vignette.
For CPM vs TMM-scaling, you'll have to consult the edgeR vignette.
"...suggest that processing the data with the estimated ("raw") counts with the edgeR pipeline has a similar effect as using scaledTPM or lengthscaledTPM"
No, raw counts alone are not similar to scaledTPM or lengthScaledTPM. It is the count + offset that gives a similar result, not count analysis alone.
"what measure would you suggest to use for calculating logFC"
The LFC estmated by DESeq2 or edgeR and returned in the results table or topTable after using any of the tximport recommended pipelines (estimated count + offset, or the counts-from-abundance option).
from tximport.
Related Issues (20)
- Outdated vignette? HOT 1
- Move Alevin import code to C++ HOT 3
- Missing release tags HOT 1
- Add option to import only whitelisted barcodes from alevin HOT 2
- ignoreAfterBar does not apply with txOut=T and countsFromAbundance != "no" HOT 1
- lose transcript names for salmon inferential replicates
- `ignoreAfterBar` not used if `txOut=TRUE` HOT 5
- cann't import kallisto abundance.h5/.tsv HOT 4
- Import processed data HOT 3
- Recomended count scaling method for DTU analysis HOT 2
- Returns TPM when abundanceCol is set to any value for type='rsem' HOT 1
- Read in files in parallel HOT 4
- Tximport issue with new R version HOT 2
- error in 1:nrow(m): argument of length 0 HOT 1
- import using tximport for the rsem count table to get integers? HOT 3
- Dealing with multispecies using tximport HOT 4
- Different length and counts depending on the number of loaded samples HOT 1
- tximport of feature counts? HOT 1
- tximport of kallisto h5s generated with multiple threads is not deterministic HOT 1
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