User: imrankhanbioinfo

Reputation:
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New User
Location:
Canada/London/Western University
Twitter:
ImrankhanUWO
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Google Scholar Page
Last seen:
1 day, 21 hours ago
Joined:
9 months, 2 weeks ago
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i***************@gmail.com

Posts by imrankhanbioinfo

<prev • 11 results • page 1 of 2 • next >
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Answer: A: How to pull pairwise comparison results after running DESeq() with more than two
... I see its working. I did not check the padj. values which is different in all comparisons. Thank you very much! ...
written 5 weeks ago by imrankhanbioinfo10
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Comment: C: How to pull pairwise comparison results after running DESeq() with more than two
... This is what I did. dds<-DESeqDataSetFromMatrix(countData=countData, colData=metaData, design=~Condition, tidy=TRUE) dds_res2<-DESeq(dds) results(dds_res2, contrast = c("Cond ...
written 5 weeks ago by imrankhanbioinfo10
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How to pull pairwise comparison results after running DESeq() with more than two condition
... Hi there, I am running into this issue of pulling pairwise comparison from more than two conditions. In my metadata file, I have 4 conditions (control, treatment A, treatment B, treatment C). I run DESeq() using these all in the experiment design. Now, I like to pull only pairwise comparison betwee ...
R rna-seq written 5 weeks ago by imrankhanbioinfo10
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Comment: A: DeSeq2 error: Every gene contains at least one zero, cannot compute log geometri
... Thanks, Kevin and swbarnes2 for your replies, Kevin your reply was the right solution. This helps us not to remove any sample during this analysis. So adding a pseudo-count value of '1' to each entry in my data helps to resolve this error. Best regards: Imran ...
written 6 weeks ago by imrankhanbioinfo10
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DeSeq2 error: Every gene contains at least one zero, cannot compute log geometric means
... Hi there, When I am running the DESeq pipeline on the dds object and getting this error message. > dds_res<-DESeq(dds_PvsN) estimating size factors Error in estimateSizeFactorsForMatrix(counts(object), locfunc = locfunc, : every gene contains at least one zero, cannot compute log geometri ...
rna-seq written 6 weeks ago by imrankhanbioinfo10
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Comment: C: DeSeq2 error: counts matrix should be numeric, currently it has mode: character
... My apologies. I was not aware of this regulation. Will comply with 100% and fully noted for the future as well. ...
written 7 weeks ago by imrankhanbioinfo10
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(Closed) DeSeq2 error: counts matrix should be numeric, currently it has mode: character
... Hi there, Is there any way to get rid of this while creating object for Deseq2. I used script: dds <- DESeqDataSetFromMatrix(countData = cts, colData = coldata, design = ~ condition) Error in DESeqDataSet(se, design = design, ignoreRank) : counts ...
R deseq2 rna-seq written 7 weeks ago by imrankhanbioinfo10 • updated 7 weeks ago by felipead6660
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Answer: C: Error: could not find function "DESeqDataSet" from DESeq2
... Thank you very much for your help. It works now. I used sessioninfo() and get my answer. There was some issue with my Rstudio and the complete installation of DeSeq2. Some packages were unable to install with the DeSeq2, so I have to do it separately. ...
written 7 weeks ago by imrankhanbioinfo10
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Error: could not find function "DESeqDataSet" from DESeq2
... Hi Guys, I am encountering an error when creating dds (DESeqDataSet). I was running DeSeq one day back everything was good but now I am having some issues like not able to find some function. I suspect its coz of my R studio (Ver. 1.2.5033). What do you think? After loading some packages I can't acc ...
gene R rna-seq written 7 weeks ago by imrankhanbioinfo10 • updated 7 weeks ago by Kevin Blighe61k
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Comment: C: Replace column name in data-frame
... X1 X2 X3 X4 X5 X6 X6 X7 Patient_id Condition tcga_counts A1BG A1CF A2BP1 A2LD1 A2ML Thank you. Here is my question. I wanted to paste a screenshot but I can't see any possibility. Anyways 1) I got more than ...
written 8 weeks ago by imrankhanbioinfo10

Latest awards to imrankhanbioinfo

Scholar 7 weeks ago, created an answer that has been accepted. For C: Error: could not find function "DESeqDataSet" from DESeq2

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