User: Anitha Sundararajan

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Posts by Anitha Sundararajan

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Comment: C: DEXSeq- fitDispersionFunction error
... I re-ran some steps so you can see the output- Please see complete code below- ============================ >source("http://bioconductor.org/biocLite.R") >biocLite("DEXSeq") >library ("DEXSeq") >library("parallel") >sampleTable.conVsgigi <- data.frame (row.names=c("control ...
written 4.2 years ago by Anitha Sundararajan140
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DEXSeq- fitDispersionFunction error
... Hello- Has anyone seen the following error before with DEXSeq? I have run the tool a couple times before with no issues. So when I try to run the "fitDispersionFunction", I get the following: *no CR dispersion estimations found, please first call estimateDispersions function* I actually ran the ...
written 4.2 years ago by Anitha Sundararajan140
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Answer: A: DEXSeq- fitDispersionFunction error
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written 4.2 years ago by Anitha Sundararajan140
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Comment: C: DEXSeq- ExonCountSet
... Thanks so much for your response(s) I went back a did a couple of things and looks like I now have the exon count set. So I was running R in the same directory as the file(s) location. I still went ahead and specified the complete path for each file and I still got the same error message. I then ...
written 4.5 years ago by Anitha Sundararajan140
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Comment: C: DEXSeq- ExonCountSet
... Thanks Jim! I should have noticed that. I had to import paths for R, gcc and other libs and re-load the package. That solved it. But I am running into another problem at the same step. When I run ecs <- read.HTSeqCounts(sampleTable$countFile, sampleTable, "Arabidopsis_thaliana.modified.flatt ...
written 4.5 years ago by Anitha Sundararajan140
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Comment: C: DEXSeq- ExonCountSet
... Thanks Jim! I should have noticed that. I had to import paths for R, gcc and other libs and re-load the package. That solved it. But I am running into another problem at the same step. When I run ecs <- read.HTSeqCounts(sampleTable$countFile, sampleTable, "Arabidopsis_thaliana.modified.flatt ...
written 4.5 years ago by Anitha Sundararajan140
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DEXSeq- ExonCountSet
... Hi I am a new user to DEXSeq and I was wondering if I could get some help resolving an error message I repeatedly get. I have my sample table and it looks like: > sampleTable countFile condition meiocyte1 Col-meiocyte-1.counts meiocytes meiocyte2 Col-meiocyte-2.counts me ...
dexseq written 4.5 years ago by Anitha Sundararajan140
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Answer: A: DEXSeq- ExonCountSet
... Hi I am a new user to DEXSeq and I was wondering if I could get some help resolving an error message I repeatedly get. I have my sample table and it looks like: > sampleTable countFile condition meiocyte1 Col-meiocyte-1.counts meiocytes meiocyte2 Col-meiocyte-2.counts me ...
written 4.5 years ago by Anitha Sundararajan140
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DEXSeq- dexseq_prepare_annotation.py error
... Hi I am trying to run dexseq_prepare_annotation.py on a gtf file (Ensembl version) downloaded from iGenomes. The organism is Arabidopsis thaliana. I am constantly getting error messages that look like this: Traceback (most recent call last): File "/home/as/R/x86_64-unknown-linux-gnu- library/ ...
organism written 4.5 years ago by Anitha Sundararajan140 • updated 4.5 years ago by Simon Anders3.5k
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Comment: C: DiffBind -error with dba.counts
... Hi Gordon Please see below the session info: > sessionInfo() R version 3.0.1 (2013-05-16) Platform: x86_64-apple-darwin10.8.0 (64-bit) locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] parallel stats graphics grDevices utils datas ...
written 5.1 years ago by Anitha Sundararajan140

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