User: bioprog

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bioprog0
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Posts by bioprog

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Comment: C: DESeq2: add annotations (from data frame) to DESeqDataSet
... thanks, i tried that and lost most of my packages unfortunately due to the fact it wont work with the upgraded version of R! Anyway, in my current version ,can i at least output a table iwht the normalized counts for each samples along with the log2 fold and p values? ...
written 3.9 years ago by bioprog0
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Answer: A: DESeq2: add annotations (from data frame) to DESeqDataSet
...     .   ...
written 3.9 years ago by bioprog0
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Comment: C: DESeq2: add annotations (from data frame) to DESeqDataSet
... No, i am using 1.6.3 apparently when checking by: packageVersion("DESeq2") [1] ‘1.6.3’ To try to get 1.10, i first removed DESeq2 using remove.packages('DESeq2') then source("http://bioconductor.org/biocLite.R") biocLite('DESeq2') then reloaded R and the DESeq2, but i still got 1.6.3 Here's my ...
written 3.9 years ago by bioprog0
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Answer: A: DESeq2: add annotations (from data frame) to DESeqDataSet
... I tried the above steps but i cant get it to work to add my features. Here is what I tried: dds <- DESeqDataSetFromMatrix(countData = countData, colData = colData, design = ~ condition) dds$condition <- relevel(dds$condition, "WT") dds <- DESeq(dds) #Add Feature data featureData <- ...
written 3.9 years ago by bioprog0
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Comment: C: chromosome name in summarizeOverlaps for RNASeq data
... I understand where you are coming from and you are right. I should have tried seqlevels on BamLst after the change before posting. I did now and that didn't seem to fix the problem. I did go over the vignette in summarizedOverlaps but that didn't seem to help me fix the issue. I will look more into ...
written 3.9 years ago by bioprog0
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Answer: A: chromosome name in summarizeOverlaps for RNASeq data
...   Thank you for your reply regarding the save and load of RDS. that fixed it. In regards to the chromosome names, can you please confirm if my understanding is correct: If I write old <- seqlevels(bamLst_grp1), I get: [1] "1"  "10" "11" "12" "13" "14" "15" "16" "17" "18" "19" "2"  "3"  "4"  "5 ...
written 3.9 years ago by bioprog0
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chromosome name in summarizeOverlaps for RNASeq data
...    For a while I used quantile normalization followed by t-test or cuffdiff for analysis of RNASeq. I would like to try DESeq2 given its better normalization method based on the readings. I am using your R package summarizeOverlaps to create count tables as I found it to be the easiest. However, I ...
rnaseq annotation counts summarizeoverlaps written 3.9 years ago by bioprog0
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Answer: A: GenomicAlignments is too slow with summarizeOverlaps
... Thanks Valerie- I think you make a good point. I will try to run things with 2 workers and yield size 100000 and see how it goes. I will look more into BiocParallel ro run the analysis as well. Thanks a lot!    ...
written 4.9 years ago by bioprog0
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Answer: A: GenomicAlignments is too slow with summarizeOverlaps
... Thank you Valerie for your feedback. It finally worked. What i did is I used worker=1 and had the run go overnight. It worked without interruptions. I checked it 7 hours later and the results were there (it probably took less time). I maintained the yieldSize as 100000. I guess it is best to run it ...
written 4.9 years ago by bioprog0
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Comment: C: GenomicAlignments is too slow with summarizeOverlaps
... thanks Valerie- I will try all algorithms then summarize my findings here so that it may be of use to others. Much appreciated. ...
written 4.9 years ago by bioprog0

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Popular Question 3.9 years ago, created a question with more than 1,000 views. For GenomicAlignments is too slow with summarizeOverlaps

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