User: aditi

gravatar for aditi
aditi20
Reputation:
20
Status:
New User
Location:
Indian Institute of Science,Bangalore, India
Last seen:
9 months ago
Joined:
3 years, 2 months ago
Email:
a****@cns.iisc.ernet.in

Posts by aditi

<prev • 13 results • page 1 of 2 • next >
2
votes
0
answers
315
views
0
answers
'Error in summary(lm1)$coefficients[2, 1] : subscript out of bounds' while running pickSoftThreshold in WGCNA
... I have successfully run WGCNA on an expression matrix. WGCNA has also worked for other sets of expression data. I am now trying to run WGCNA on the first PC, PC1-2 and PC1-3 of the same expression matrix. However, I am unable to get past picking soft threshold for the new matrices. Where am I going ...
wgcna picksoftthreshold written 13 months ago by aditi20
0
votes
1
answer
370
views
1
answer
Extract sequences corresponding to TCONS IDs from spliceR
... Hi, I have GTF files from spliceR which tell me which transcripts of certain genes are differentially expressed between different conditions. However, I am unable to find what the ids assigned to the transcripts (TCONS) correspond to. Is there a way to extract the transcript sequences corresponding ...
splicer written 16 months ago by aditi20 • updated 16 months ago by k.vitting.seerup90
0
votes
11
answers
6.4k
views
11
answers
Comment: C: readCufflinks problem with extdata
... I'm facing the same issue. I too see that older cuffdiff output works well with cummeRbund but not the more recent cuffdiff output. The suggestions given here did not work for me. Is there an update on the issue?   ...
written 16 months ago by aditi20
0
votes
1
answer
433
views
1
answers
Answer: A: Increased number of total exons in DEXSeq
... Thanks! How can I solve this? ...
written 2.2 years ago by aditi20
0
votes
1
answer
433
views
1
answer
Increased number of total exons in DEXSeq
... Hi, I have aligned RNA-Seq data from human samples to GRCh37. The flattened file has also been created using the same database using the dexseq_prepare_annotation.py and the counts have been generated using the dexseq_counts.py script. However, the total number of exon for most of the genes are gre ...
dexseq grch37 exons written 2.2 years ago by aditi20
0
votes
1
answer
1.2k
views
1
answers
Answer: A: Error in strsplit() : non-character argument - using DEXSeq
... Hi Sakura, Your count files seem to be full of empty counts(9million seems too high). If your library is strand specific I'm guessing that you must have taken care of the defining the library type during the alignment (firststrand or secondstrand if you used tophat, that is). Also, with some librar ...
written 3.1 years ago by aditi20
0
votes
1
answer
860
views
1
answers
Comment: C: DexSeq extracols option
... Hi Ioannis, It might sound stupid but does the data.frame that is used with extraCols need to have the exonBaseMean, dispersion, counts and all the other details that the DEXSeqHTML object has? I followed the steps that you mentioned and could successfully incorporate the genenames and symbols in t ...
written 3.1 years ago by aditi20
0
votes
2
answers
3.9k
views
2
answers
Comment: C: biomaRt no longer works with proxy after upgrade
... Hi! I am facing a similar issue with biomaRt. I'm working behind a proxy and have modified the Renviron file to incorporate the proxy addresses and port. I have also used the RCurlOptions to feed in the proxy as suggested in the biomart vignette. I am using the useMart command as suggested by Johan ...
written 3.1 years ago by aditi20
0
votes
1
answer
1.7k
views
1
answers
Comment: C: DEXSeq Error in estimateExonFoldChanges: the matrix is either rank-deficient or
... Sorry! I guess I didn't run the command right! I'm a complete novice in this field. The output is a series of ensembl ids: [99990] "ENSMUSG00000027397:E014"                                                                                                [99991] "ENSMUSG00000027397:E015"               ...
written 3.2 years ago by aditi20
0
votes
1
answer
1.7k
views
1
answers
Comment: C: DEXSeq Error in estimateExonFoldChanges: the matrix is either rank-deficient or
... > rownames(dxd)[which(x)] character(0) ...
written 3.2 years ago by aditi20

Latest awards to aditi


Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 138 users visited in the last hour