User: minie

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minie0
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Posts by minie

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Comment: C: DESeq2 different versions
... Oh but I am sure I have used the option, anyways I am planning to perform the analysis with different versions using some more datasets I will write you back with the results. May be not here with huge gene lists and stuff. ...
written 11 months ago by minie0
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Comment: C: DESeq2 different versions
... I have removed the v 1.16 and I am currently wroking with other version of DESeq2 to maintain consistency for some  old stuff.I am not sure how long it will take for me to redo the installation and analysis, in any case without that can you give some inputs if possible no hurry its just that I notic ...
written 11 months ago by minie0
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Comment: C: DESeq2 different versions
... Thanks for your input ,I wil get back to you for values later: Chunk of code  I am using, is following: dds <- DESeqDataSetFromHTSeqCount( sampleTable = pdata, design= (~ group)) dds <- DESeq(dds) resultsNames(dds) res = result(dds, contrast=c("group","B","A") reslfc = lfcshrink(dds, coef ...
written 11 months ago by minie0
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Comment: C: DESeq2 different versions
... Thanks for your input. Examples : gene A(v10)= 1.79 , gene A(v14)= 2.23 , gene A(v16)= 6.09 Also, I was thinking might be there are some other additional factors which are adding up to the shrinkage and causing such variations while using different versions? Do you think something like this is poss ...
written 11 months ago by minie0
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Comment: C: DESeq2 different versions
... I am not sure what more specific you want ? please elaborate. I have already stated in the first sentence values obtatined are varying.Offcourse contrasts provided was same while analysing the data using all the three versions. if you read my first post its clearly mentioned I have used lfcshrink an ...
written 11 months ago by minie0
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DESeq2 different versions
... I have analysed the data using three different versions of DESeq2  v.1.10, v.1.14 & v.1.16 values are varying even after using  lfcShrink and betaprior=TRUE while using v.1.16 v.1.10 & v1.14 involves shrinkage and by default while v.1.16 do not. I presumed that shrinkage method in all the v ...
rnaseq deseq2 R written 11 months ago by minie0 • updated 11 months ago by Michael Love19k
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Comment: C: R packages old versions
... Thanks. It's really helpful. ...
written 11 months ago by minie0
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R packages old versions
... Where to find the repository for DESeq2 old version, for manual installation ...
deseq2 R package written 11 months ago by minie0 • updated 11 months ago by Michael Love19k
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Answer: A: GenomicFeatures package ERROR
... Is there a way to export the gtf file from GenomicRanges I have calculated intron coordinates from gtf file using exon coordinates and now I need to export it from the range , I tried following code but getting an error:   export.gtf(introns,"introns.gtf",format ="gtf") Error in export.gtf(intron ...
written 16 months ago by minie0
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Answer: A: BS genome non-model organism
... Hi Thanks for this ,but I have a trouble calling this twobitFa file to DESeq2 package. Can you tell me is there any way to do it??       ...
written 19 months ago by minie0

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