Error in reading data on isoformswitchanalyzeR
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@saddamhusain77-19420
Last seen 2.5 years ago

I am trying to figure out how to use IsoformSwitchAnalyzeR on Salmon quantification. I'm really stuck at the very beginning. I have not been able to import the data. Below is the code I am using-

getwd()

[1] "/Users/saddamhusain/Desktop/salmon_isoswitch"

salmonQuant <- importIsoformExpression(

  • parentDir = system.file("salmonQuant", package="IsoformSwitchAnalyzeR")

  • )

Step 1 of 3: Identifying which algorithm was used...

Error in dirList[sapply(dirList, FUN = function(aDir) { :

invalid subscript type 'list'

salmon_isoswitch is a directory that contains salmonQuant subdirectory that in tern contains four independent subdirectories for each sample.

Any help will be appreciated.

isoformswitchanalyzeR rna-seq splice-variants • 736 views
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With this code-

salmonQuant <- importIsoformExpression("salmonQuant")

Step 1 of 3: Identifying which algorithm was used...

Error in importIsoformExpression("salmonQuant") : No directories of interest were found

Even though .txt files of count data are there.

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Can you work through the example data successfully first?

https://bioconductor.org/packages/release/bioc/vignettes/IsoformSwitchAnalyzeR/inst/doc/IsoformSwitchAnalyzeR.html

I suggest reading the section in the longer workflow called ' Importing Data from Kallisto, Salmon, RSEM or StringTie'. It is pretty straightforward, I use this command, where this is simply the directory my salmon folders are in:

salmonQuant <- importIsoformExpression( parentDir = "C:/Users/chris/Desktop/isoswitcher/NewTranscriptomePEACbaseline/stringtie.salmon.v26/", addIsofomIdAsColumn = TRUE )

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Thank you chris for the response. Yes, I can work through the example data smoothly but still getting the error with my data.

salmonQuant <- importIsoformExpression( parentDir = "/Users/saddamhusain/Desktop/salmon_isoswitch/")

Step 1 of 3: Identifying which algorithm was used...

Error in importIsoformExpression(parentDir = "/Users/saddamhusain/Desktop/salmon_isoswitch/") :

No directories of interest were found

salmonisoswitch folder contains four different folders named as "helc1" "helc2" "helt1" and "hel_t2" each of which contains respective quant.txt file.

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OK, I think there is something different with your salmon output directories. I don't know what that is. Make sure your output directories contain all the files and folders normally outputted by salmon into a directory per sample.

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If you are sure your output directories are as normal (they match example ones), then ask here for more help, https://github.com/kvittingseerup/IsoformSwitchAnalyzeR/issues.

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I got quantification and gene quantification output from salmon ( v-0.13.1). I have done differential expression analysis on quantification files so I suppose same files should work out on isoformswitchanalyzer. Thanks for the suggestion. I have raised the same issue on GitHub too and am following it.

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Try doing some example read alignments and then just trying to input the directory into R. I am having no problems with it, I'm using the latest version of salmon and not changing the output folder files and structure at all afterwards.

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Thanks Chris, yeah, I will try to figure it out.

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eshelden ▴ 20
@eshelden-14132
Last seen 2.4 years ago

The function importIsoformExpression in my version of the package has the following line: supportedTypes <- data.frame(orign = c("Kallisto", "Salmon", "RSEM", "StringTie"), fileName = c("abundance.tsv", "quant.sf", "isoforms.results", "tdata.ctab"), eLengthCol = c("efflength", "EffectiveLength", "effective_length", "")

I believe your Salmon file names need to end in ".quant.sf", not ".txt" in order to be considered valid.

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