## User: bioprog

bioprog0
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#### Posts by bioprog

<prev • 15 results • page 1 of 2 • next >
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... 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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...     .   ...
written 3.9 years ago by bioprog0
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... 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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... 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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... 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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...   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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...    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 ...
written 3.9 years ago by bioprog0
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... 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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... 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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... 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

#### Latest awards to bioprog

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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