Moderator: swbarnes2
swbarnes2 ♦ 9.4k
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Posts by swbarnes2
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... With only three replicates, you can't omit that sample based solely on your visualizations. Now, if the people who made the library have evidence that that sample didn't behave right, that would allow you to omit it, but for all you know, that variance (and PC2 is only 9%) is real. ...
written 1 day ago by
swbarnes2 ♦ 9.4k
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49
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... Why don't your sets names match anything in the csv?
I'd see if `nsets` works instead. ID's also try removing "Genome_location", and just having that be blank instead. R is generally happier with row names don't have a column header. ...
written 1 day ago by
swbarnes2 ♦ 9.4k
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87
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Comment:
C: IPA pathway for DESeq2 result
... SE stands for standard error. You don't want that. ...
written 3 days ago by
swbarnes2 ♦ 9.4k
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171
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... For starters, I would not give your outputs the same name as your inputs! You need to keep inputs and outputs separate.
The simplest explanation is that not a single one of your 20-027 reads passes your filter, so you just overwrote your original file with nothing. ...
written 6 days ago by
swbarnes2 ♦ 9.4k
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76
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Comment:
A: removal batch effect
... Also, note that for finding DE genes, the typical way to handle batches is **not** to alter the counts in anyway, but to leave them as they are, and include batch as an element of the design. ...
written 6 days ago by
swbarnes2 ♦ 9.4k
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82
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Comment:
C: BWA index is not working
... First things I'd check are that the formats of your fastqs and fastqs are okay. ...
written 7 days ago by
swbarnes2 ♦ 9.4k
0
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1
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141
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... Go back and do things right with ensembl IDs. Those are always unique. ...
written 7 days ago by
swbarnes2 ♦ 9.4k
1
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1
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87
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1
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... Illumina lanes generally do not add technical variance, so you shouldn't include them in the design. ...
written 7 days ago by
swbarnes2 ♦ 9.4k
1
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123
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... The annotation is what it is. Your first example is located on a real chromosome, the second is on a scaffold, FWIW.
Just keep the ensemble IDs as the primary identifier all the way through. They are unique. ...
written 8 days ago by
swbarnes2 ♦ 9.4k
0
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65
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... No one can troubleshoot without details of your code, and no one wants to write code for you. What exactly did you try? ...
written 12 days ago by
swbarnes2 ♦ 9.4k
Latest awards to swbarnes2
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3 days ago,
created a comment with at least 3 up-votes.
For C: All of the lines in my file are part of the header / no alignment section
Appreciated
4 weeks ago,
created a post with more than 5 votes.
For A: Blast: Homology Or Similarity?
Teacher
8 weeks ago,
created an answer with at least 3 up-votes.
For A: Calculating Rpkm For Rna-Seq Data Including Several Samples Each Condition
Appreciated
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created a post with more than 5 votes.
For A: Blast: Homology Or Similarity?
Teacher
8 weeks ago,
created an answer with at least 3 up-votes.
For A: Calculating Rpkm For Rna-Seq Data Including Several Samples Each Condition
Popular Question
11 weeks ago,
created a question with more than 1,000 views.
For DESeq2 multi-factor design
Teacher
3 months ago,
created an answer with at least 3 up-votes.
For A: Calculating Rpkm For Rna-Seq Data Including Several Samples Each Condition
Teacher
3 months ago,
created an answer with at least 3 up-votes.
For A: Calculating Rpkm For Rna-Seq Data Including Several Samples Each Condition
Appreciated
3 months ago,
created a post with more than 5 votes.
For A: Blast: Homology Or Similarity?
Teacher
4 months ago,
created an answer with at least 3 up-votes.
For A: Calculating Rpkm For Rna-Seq Data Including Several Samples Each Condition
Teacher
4 months ago,
created an answer with at least 3 up-votes.
For A: Calculating Rpkm For Rna-Seq Data Including Several Samples Each Condition
Teacher
4 months ago,
created an answer with at least 3 up-votes.
For A: Calculating Rpkm For Rna-Seq Data Including Several Samples Each Condition
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