User: elb

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elb160
Reputation:
160
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Location:
Torino
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2 days, 20 hours ago
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7 years ago
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Posts by elb

<prev • 68 results • page 1 of 7 • next >
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Annotate counts region by region
... Hi guys, I know it could be an answer 1000 times redundant but I looked around without find a quick solution. I have 5 .bam files and a .gtf file that looks like this: > 1 134202951 134202953 > 1 134202954 134203590 > 1 134199215 134203590 where 1 indicates ch ...
bam chip-seq written 29 days ago by elb160
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Comment: C: edgeR and design matrix with triplicates
... Yes I know! My problem is that my samples are highly variable but as you correctly say the cross comparison of results could be affected if samples are considered in a "paired" analysis. ...
written 5 weeks ago by elb160
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Comment: C: edgeR and design matrix with triplicates
... Ohhhh wow! The answer I was looking for! Thank you very much. EdgeR does not address this point! Thank you very much! ...
written 5 weeks ago by elb160
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Comment: C: edgeR and design matrix with triplicates
... Thank you very much! I have another doubt. The estimateDisp should be done on the entire count matrix or on the subset of comparisons you want to look at? For example considering only samples in Treatment1 end Control1 on all the samples together? My point is: if you do not compare the Treatments ac ...
written 5 weeks ago by elb160
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Comment: C: edgeR and design matrix with triplicates
... No and this is why I'm asking because of some doubts ...
written 5 weeks ago by elb160
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Comment: C: edgeR and design matrix with triplicates
... the tutorial of edgeR ...
written 5 weeks ago by elb160
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edgeR and design matrix with triplicates
... Hi guys, suppose to have the following situation: > MouseA MouseB MouseC > Treatment1 Treatment1 Treatment1 > Control1 Control1 Control1 > Treatment2 Treatment2 Treatment2 > Cont ...
R edger rna-seq written 5 weeks ago by elb160 • updated 5 weeks ago by ATpoint19k
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Preranked GSEA statistics
... Hi guys, I have a general question regarding the pre-ranked GSEA. I have a list of genes ranked according to the LogFC and then a list of genes that is my geneset. I would like to see if the genes of the geneset are enriched in my ranked list. To do this, I'm running the pre-ranked GSEA. I'm no ...
gsea written 7 weeks ago by elb160 • updated 6 weeks ago by alserg200
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LogFC calculation in multiple comparisons
... Hi guys, suppose to be in the following situation: SampleA1 SampleA2 SampleA3 Ctrl1 Ctrl2 SampleB1 SampleB2 SampleB3 234 1 32 5 2 0 21 12344 2434 134 0 2 0 0 0 ...
rna-seq edger deseq written 3 months ago by elb160 • updated 3 months ago by RamRS22k
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On the practical use of estimateDisp function
... Hi guys, I have a general question regarding the correct use of estimateDisp function of edgeR. Suppose you have the following situation: Sample Condition A1 Control A2 Control B1 Treatment1 B2 Treatment1 B3 Treatment1 ...
rna-seq edger written 3 months ago by elb160 • updated 3 months ago by RamRS22k

Latest awards to elb

Supporter 12 months ago, voted at least 25 times.
Great Question 14 months ago, created a question with more than 5,000 views. For Check For Co-Expressed Genes In Microarray Experiments
Popular Question 16 months ago, created a question with more than 1,000 views. For regulatory regions discovery and alignment
Popular Question 16 months ago, created a question with more than 1,000 views. For Transcription Factors Annotation
Great Question 4.2 years ago, created a question with more than 5,000 views. For Check For Co-Expressed Genes In Microarray Experiments
Popular Question 4.2 years ago, created a question with more than 1,000 views. For Transcription Factors Annotation
Student 4.2 years ago, asked a question with at least 3 up-votes. For Looking For Network Visualization Tools
Popular Question 6.6 years ago, created a question with more than 1,000 views. For Check For Co-Expressed Genes In Microarray Experiments
Popular Question 6.6 years ago, created a question with more than 1,000 views. For Fold Change Detection In Affymetrix Microarray Data Without Replicates
Popular Question 6.6 years ago, created a question with more than 1,000 views. For Looking For Network Visualization Tools
Student 6.6 years ago, asked a question with at least 3 up-votes. For Looking For Network Visualization Tools

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